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373 results on '"Interactions plantes-microorganismes et santé végétale"'

1. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Author: Pasqua Veronico, Emeline Deleury, Francesca De Luca, Magali Esquibet, Patrick Wincker, Thomas J. Baum, Tom R. Maier, Erika Sallet, Jonathan J. Ewbank, Edgardo Ugarte, Cyril Van Ghelder, Marie-Noëlle Rosso, Delphine Steinbach, Marie-Cécile Caillaud, Jean Weissenbach, Véronique Anthouard, Pedro M. Coutinho, Mark Blaxter, Jean-Marc Aury, Marc Robinson-Rechavi, Pierre Abad, Geert Smant, Timothé Flutre, Hadi Quesneville, Gabriel V. Markov, Paul McVeigh, Jérôme Gouzy, Philippe Castagnone-Sereno, Corinne Dasilva, Etienne Danchin, Paola Leonetti, Aaron G. Maule, Marc Magliano, Béatrice Ségurens, John T. Jones, Eric L. Davis, Laetitia Perfus-Barbeoch, Claire Jubin, Thomas Schiex, Vincent Laudet, Florence Deau, Olivier Jaillon, François Artiguenave, Eric Grenier, Tarek Hewezi, Bruno Favery, Teresa Bleve-Zacheo, T.O.G. Tytgat, Bernard Henrissat, Noureddine Hamamouch, Graziano Pesole, Jared V. Goldstone, Julie Poulain, Vivian C. Blok, Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Scottish Crop Research Institute, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Istituto per la Protezione delle Piante, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Unité de Recherche Génomique Info (URGI), Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), Department of Plant Pathology, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Iowa State University (ISU), School of Biological Sciences, Dipartimento di Biochimica e Biologia moleculare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Department of Ecology and Evolution, Université de Lausanne = University of Lausanne (UNIL), Laboratory of Nematology, Wageningen University and Research [Wageningen] (WUR), Institute of Evolutionary Biology, University of Edinburgh, University of North Carolina System (UNC), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, School of Biolgical Sciences, Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 1064 UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Institut National de la Recherche Agronomique (INRA)-Santé des plantes et environnement (S.P.E.)-UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Consiglio Nazionale delle Ricerche [Roma] (CNR), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Università degli studi di Bari, Université de Lausanne (UNIL), Wageningen University and Research Centre [Wageningen] (WUR), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Unité de Biométrie et Intelligence Artificielle (UBIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Università degli studi di Bari Aldo Moro (UNIBA)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Helminth genetics, 01 natural sciences, Applied Microbiology and Biotechnology, Genome, Plant Roots, Meloidogyne incognita, ADAPTATION, genes, root-knot nematodes, Genes, Helminth, 2. Zero hunger, Expressed Sequence Tags, 0303 health sciences, biology, plant-parasitic nematode, EPS-2, Chromosome Mapping, GENOME SEQUENCE, food and beverages, DNA, Helminth, Plants, bdelloid rotifers, MELOIDOGYNE INCOGNITA, PARTHENOGENETIC NEMATODE, Molecular Medicine, RNA Interference, Terra incognita, Biotechnology, DNA, Complementary, Sequence analysis, Molecular Sequence Data, Biomedical Engineering, cloning, Bioengineering, phytopathogenic bacteria, 03 medical and health sciences, Botany, expression, Animals, Tylenchoidea, Gene, Laboratorium voor Nematologie, 030304 developmental biology, Plant Diseases, Whole genome sequencing, PLANT PARASITISM, Genome, Helminth, Base Sequence, Sequence Analysis, DNA, prediction, biology.organism_classification, caenorhabditis-elegans, Nematode, Evolutionary biology, identification, Laboratory of Nematology, protein, Sequence Alignment, 010606 plant biology & botany
Abstract: Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies
Published: 2008

2. Root-knot nematodes manipulate plant cell functions during a compatible interaction

Author: Marie-Cécile Caillaud, Philippe Lecomte, Bruno Favery, Pierre Abad, Marie-Noëlle Rosso, Géraldine Dubreuil, Michaël Quentin, Laetitia Perfus-Barbeoch, Janice de Almeida Engler, Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), UMR 1064 UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Institut National de la Recherche Agronomique (INRA)-Santé des plantes et environnement (S.P.E.)-UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale (IPMSV), and Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)
Subjects: 0106 biological sciences, Cell division, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, 01 natural sciences, Host-Parasite Interactions, 03 medical and health sciences, Multinucleate, RNA interference, Botany, Plant defense against herbivory, Animals, Endoreduplication, Tylenchoidea, Arabidopsis Genomics Giant cells Meloidogyne root-knot nematode Pathogenicity factors, Plant Diseases, 030304 developmental biology, 0303 health sciences, biology, food and beverages, biology.organism_classification, Plant cell, Cell biology, Nematode, Giant cell, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Sedentary endoparasitic nematodes are root parasites that interact with their hosts in a remarkable way. These obligate biotrophic pathogens establish an intimate relationship with their host plants, inducing the redifferentiation of root cells into specialized feeding cells. The successful establishment of feeding cells is essential for nematode development. Root-knot nematodes, of the genus Meloidogyne, have evolved strategies enabling them to induce feeding cell formation in thousands of plant species, probably by manipulating fundamental elements of plant cell development. Feeding cells enlarge and are converted into multinucleate giant cells through synchronous nuclear divisions without cell division. Fully differentiated giant cells may contain more than a hundred polyploid nuclei that may have undergone extensive endoreduplication. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of the typical root gall. Giant cell formation requires extensive changes to gene expression. The induction of feeding cells remains poorly understood, but it is thought that effectors secreted by the nematode play a key role in parasitism, with potential direct effects on recipient host cells. In this review, we focus on the most recent investigations of the molecular basis of the plant–root-knot nematode interaction. Recently, microarray technology has been used to study the plant response to Meloidogyne spp. infection. Such a genome-wide expression profiling provides a global view of transcriptional changes, especially for genes involved in cell wall, transport processes and plant defense responses during giant cell formation. The identification of nematode-responsive plant genes constitutes a major step toward understanding how root-knot nematodes dramatically alter root development to induce and maintain giant cells. The characterization of nematode secretions as parasitism effectors and the development of RNAi technology should improve our understanding of the molecular events and regulatory mechanisms involved in plant parasitism. Finally, Meloidogyne genome sequences should provide further insight into plant–root-knot nematode interactions.
Published: 2008

3. Elicitin Genes Expressed In Vitro by Certain Tobacco Isolates of Phytophthora parasitica Are Down Regulated During Compatible Interactions

Author: Colas , F, Conrod , Sandrine, VENARD , Paul, Keller , Harald, Ricci , Pierre, Panabières , Franck, Colas , Virginie, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en neurobiologie - neurophysiologie de Marseille ( CRN2M ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Sophia Agrobiotech [Sophia Antipolis] ( ISA ), Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut National de la Recherche Agronomique ( INRA ), Interactions Plantes Microorganismes et Santé Végétale, Institut National de la Recherche Agronomique ( INRA ), UR 0254 Unité de recherche Génétique et Amélioration des Plantes, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)
Subjects: Phytophthora, 0106 biological sciences, Hypersensitive response, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Physiology, [SDV]Life Sciences [q-bio], Nicotiana tabacum, Molecular Sequence Data, Down-Regulation, Virulence, Enzyme-Linked Immunosorbent Assay, Biology, 01 natural sciences, Microbiology, 03 medical and health sciences, Solanum lycopersicum, Sequence Homology, Nucleic Acid, Tobacco, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, DNA, Fungal, Pathogen, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Base Sequence, [ SDV ] Life Sciences [q-bio], Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, Algal Proteins, fungi, Proteins, food and beverages, Elicitin, General Medicine, Phytophthora nicotianae, Blotting, Northern, biology.organism_classification, 3. Good health, Plants, Toxic, POUVOIR PATHOGENE, Agronomy and Crop Science, Systemic acquired resistance, 010606 plant biology & botany
Abstract: International audience; Phytophthora spp. secrete proteins called elicitins in vitro that can specifically induce hypersensitive response and systemic acquired resistance in tobacco. In Phytophthora parasitica, the causal agent of black shank, most isolates virulent on tobacco are unable to produce elicitins in vitro. Recently, however, a few elicitin-producing P. parasitica strains virulent on tobacco have been isolated. We investigated the potential diversity of elicitin genes in P. parasitica isolates belonging to different genotypes and with various virulence levels toward tobacco as well as elicitin expression pattern in vitro and in planta. Although elicitins are encoded by a multigene family, parAl is the main elicitin gene expressed. This gene is highly conserved among isolates, regardless of the elicitin production and virulence levels toward tobacco. Moreover, we show that elicitin-producing P. parasitica isolates virulent on tobacco down regulate parAl expression during compatible interactions, whichever host plant is tested. Conversely, one elicitin-producing P. parasitica isolate that is pathogenic on tomato and avirulent on tobacco still expresses parAl in the compatible interaction. Therefore, some P. parasitica isolates may evade tobacco recognition by down regulating parA1 in planta. The in planta down regulation of parA1 may constitute a suitable mechanism for P. parasitica to infect tobacco without deleterious consequences for the pathogen.
Published: 2001

4. Ca2+-dependent lipid binding and membrane integration of PopA, a harpin-like elicitor of the hypersensitive response in tobacco

Author: Racape, J., Belbahri, L., Engelhardt, S., Lacombe, B., Lee, J., Lochman, J., Marais, A., Nicole, M., Nurnberger, T., Parlange, F., Puverel, S., Keller, H., Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry (IPB), Department of Biochemistry, Faculty of Science, Masaryk University [Brno] (MUNI), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Réponse des Organismes aux Stress Environnementaux (ROSE), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), CSM, Centre Scientifique de Monaco, Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA), Eberhard Karls Universität Tübingen, Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Masaryk University, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Interactions plantes-microorganismes et santé végétale ( IPMSV ), Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Leibniz Institute of Plant Biochemistry, Diversité et génomes des plantes cultivées ( DGPC ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut National de la Recherche Agronomique ( INRA ), Réponse des Organismes aux Stress Environnementaux ( ROSE ), and Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA )
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, ralstonia-solanacearum, bacterial pathogenesis, plant-pathogen, transgenic tobacco, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, secondary structure, iii secretion system, yersinia-enterocolitica, effector protein, structure prediction, programmed cell-death
Abstract: PopA is released by type III secretion from the bacterial plant pathogen Ralstonia solanacearum and triggers the hypersensitive response (HR) in tobacco. The function of PopA remains obscure, mainly because mutants lacking this protein are not altered in their ability to interact with plants. In an attempt to identify the site of PopA activity in plant cells, we generated transgenic tobacco plants expressing the popA gene under the control of an inducible promoter. Immunocytologic analysis revealed that the HR phenotype of these plants correlated with the presence of PopA at the plant plasma membrane. Membrane localization was observed irrespective of whether the protein was designed to accumulate in the cytoplasm or to be secreted by the plant cell, suggesting a general lipid-binding ability. We found that the protein had a high affinity for sterols and sphingolipids in vitro and that it required Ca2+ for both lipid binding and oligomerization. In addition, the protein was integrated into liposomes and membranes from Xenopus laevis oocytes where it formed ion-conducting pores. These characteristics suggest that PopA is part of a system that aims to attach the host cell plasma membrane and to allow molecules cross this barrier.
Published: 2005

5. Integrative taxonomy of Meloidogye ottersoni (Thorne, 1969) Franklin, 1971 (Nematoda: Meloidogynidae) parasitizing flooded rice in Brazil

Author: Leite, Raycenne Rosa, Gomes, Ana Cristina M. M., Py, Leandro Grimaldi, Leite, Raycenne, Mattos, Vanessa, Gomes, Ana, Py, Leandro, Souza, Daniela, Castagnone-Sereno, Philippe, Cares, Juvenil, Carneiro, Regina, Universidade de Brasilia [Brasília] (UnB), Embrapa Recursos Genéticos e Biotecnologia [Brasília], Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ), and Embrapa Genetic Resources and Biotechnology and Research Foundation of the Federal District (FAPDF) 193.001.167/2015
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, 0301 basic medicine, root-knot nematode, [SDV]Life Sciences [q-bio], Population, Plant Science, Horticulture, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, 03 medical and health sciences, Graminicola, morphology, Botany, D2D3, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Canary grass, COXII, education.field_of_study, Oryza sativa, biology, esterase phenotyping, Oryza, Parthenogenesis, Phalaris arundinacea, biology.organism_classification, 030104 developmental biology, Nematode, Taxonomy (biology), ITS, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; A root-knot nematode (RKN) parasitizing rice (Oryza sativaL.) and causing damage in Santa Catarina (SC), Rio Grande do Sul (RS) and Parana (PR) states (Brazil) was identified asMeloidogyne ottersoni(Thorne1969) Franklin1971. The species is redescribed from the Brazilian population from Meleiro (SC) and compared with the description ofM. ottersonifrom Wind Lake (Wisconsin, USA) with additional morphological, biochemical and molecular characterization. The female and male bear smaller stylets: 10-12 mu m, 14-16 mu m, respectively, when compared withM. graminicola: 12-14 mu m, 16-18 mu m, andM. oryzae: 14-16 mu m, 18-20 mu m.Meloidogyne ottersonipresents perineal patterns located on the contour of a slight protuberance. Striae are mostly continuous, never raised by transverse irregular striae, as frequently observed inM. graminicolaandM. oryzae.Meloidogyne ottersonibelongs to the RKN group 11 described by Jepson (1987); the reproduction is by meiotic parthenogenesis and the somatic chromosome number is 18. The tail of second-stage juveniles is very long and thin, and tapers to a long, narrow, irregular hyaline terminus (M. ottersoni, 20.5 mu mvs M. graminicola,17.9 mu m andM. oryzae, 22.0 mu m, respectively). The ability of the BrazilianM. ottersonipopulation to parasitize canary grass,Phalaris arundinaceaL. (type host), and barnyard grass,Echinocloa crus-galli,was confirmed. Biochemically, the esterase profile ofM. ottersonilacks any band (Est Ot0, Rm=0), which differentiates it fromM. graminicolaandM. oryzae(Est VS1, Rm=0.70 and Est O1,Rm=1.02, respectively). In Maximum Likelihood analysis of ITS, D2D3 and COXII-16S rRNA sequences, populations ofM. ottersonifrom different states of Brazil clustered together and were separated from otherMeloidogynespp., thus confirming that all four populations are very similar and conspecific.
Published: 2020

6. Integrative taxonomy of Meloidogye ottersoni (Thorne, 1969) Franklin, 1971 (Nematoda: Meloidogynidae) parasitizing flooded rice in Brazil

Author: Mattos, Vanessa, Gomes, Ana Cristina M. M., Souza, Daniela, Cares, Juvenil, Leite, Raycenne Rosa, Mattos, Vanessa S., M.M.Gomes, Ana Cristina, Py, Leandro Grimaldi, Souza, Daniela A., Castagnone-Sereno, Philippe, Cares, Juvenil E., Carneiro, Regina M. D. G., Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Published: 2020

7. First Report of Alfalfa mosaic virus in Pachysandra terminalis in Europe

Author: L. Cardin, Benoît Moury, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Unité de Pathologie Végétale (PV), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, viruses, Plant Science, 01 natural sciences, Vigna, 03 medical and health sciences, Plant virus, Botany, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Chenopodium, fungi, food and beverages, Pachysandra terminalis, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Horticulture, Alfalfa mosaic virus, Pachysandra, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Myzus persicae, Aphis craccivora, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Pachysandra terminalis (Buxaceae) was introduced from Japan to Europe in 1882. This ornamental plant is grown in northern Europe as a ground cover in shaded sites. Line patterns, more or less necrotic ringspots, and mosaic symptoms on leaves of pachysandra plants have been seen in public gardens in France (Strasbourg, Colmar, Mulhouse, and Nantes) and Germany (Freiburg im Breisgaü). Extracts of plant tissues obtained from these five sites were used for mechanical- and aphid-transmission experiments, enzyme-linked immunosorbent assays (ELISA) with antibodies directed toward a tomato strain of Alfalfa mosaic virus (AMV) (from G. Marchoux, INRA, France), and electron microscopy. All inoculations produced symptoms typical for AMV in Nicotiana tabacum cv. Xanthi-nc tobacco, Chenopodium amaranticolor, C. quinoa, Vigna unguiculata, Phaseolus vulgaris, Vicia faba, Pisum sativum, and Ocimum basilicum (2). Moreover, Medicago arborea, a new host for AMV, showed systemic mosaic on leaflets. On these and the original pachysandras, AMV was readily detected by ELISA. After isolation from three to four local lesions on Vigna unguiculata and further multiplication in tobacco, one isolate was purified. Bacilliform particles of three sizes, typical for AMV, were seen by electron microscopy. Transmissions of the strain to ELISA-negative pachysandras was achieved by mechanical inoculations (7 of 20 inoculated plants were ELISA positive) and by the aphid species Myzus persicae and Aphis craccivora (14 of 17 inoculated plants were infected). Symptoms were observed 2 months after inoculation; some of the plants remained symptomless but were AMV positive in ELISA. As early as 1970, similar symptoms were reported in pachysandra in New Jersey, and AMV was isolated from affected plants (1). However, inoculations of healthy pachysandra plants with AMV was not performed. Our results show the need for an AMV indexing protocol in the propagation of pachysandra to control its spread. References: (1) D. E. Hershman and E. H. Varney. Plant Dis. 66:1195, 1982. (2) E. M. J. Jaspars and L. Bos. 1980. Alfalfa mosaic virus. No. 229 in: Descriptions of Plant Viruses. Commonw. Mycol. Inst./Assoc. Appl. Biol., Kew, England.
Published: 2019

8. First Report of Alfalfa mosaic virus in Physostegia virginiana

Author: L. Cardin, J. P. Onesto, Benoît Moury, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Unité de Pathologie Végétale (PV), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 2. Zero hunger, Aphid, biology, Inoculation, fungi, food and beverages, Plant Science, Physostegia, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Vigna, Horticulture, Alfalfa mosaic virus, Plant virus, Ornamental plant, Botany, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Myzus persicae, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Physostegia virginiana Benth. (false dragon head) is a perennial plant from the family Lamiaceae cultivated as an ornamental in gardens and for cut-flower production. In 2000, stunting of plants and yellow-to-brown ringspots on leaves were observed in cut-flower production in the Alpes Maritimes Department (southeast France). These symptoms greatly decreased the commercial value of the stems. The disease was attributed to Alfalfa mosaic virus (AMV) because extracts of infected plant tissues revealed typical bacilliform particles by electron microscopy, produced symptoms typical of AMV after inoculation of a range of previously described test plants (1), and reacted positively in enzyme-linked immunosorbent assays (ELISA) with antibodies raised to a tomato strain of AMV (from G. Marchoux, INRA, France). After isolation from single local lesions on Vigna unguiculata, the AMV isolate was multiplied in cv. Xanthinc tobacco, where it induced local and systemic ringspot symptoms. Infected Xanthinc plants served as sources of inocula for subsequent mechanical- and aphid (Myzus persicae)-transmission tests to healthy seedlings of P. virginiana (seeds from the botanic garden of Nancy, France; 36 plants for each inoculation procedure). Chlorotic and necrotic local lesions were observed in 25% of mechanically inoculated plants. Three months after inoculation, uninoculated leaves of all mechanically inoculated plants and 30.5% of aphid-inoculated plants tested positive for AMV based on ELISA. During the first year after inoculation, less than 10% of infected plants showed typical systemic symptoms. This proportion reached 40% during the second year. Recently, we observed similar symptoms in P. virginiana plants cultivated in public gardens in Intercourse (Pennsylvania), Toronto (Ontario, Canada) and Montreal (Quebec, Canada). Using ELISA, AMV was detected in symptomatic plants from these three additional locations. Reference: (1) L. Cardin and B. Moury. Plant Dis. 84:594, 2000.
Published: 2019

9. Genome sequence of the cluster root forming white lupin;

Author: Barbara Hufnagel, Benjamin Péret, Pierre-Marc Delaux, Patrick Doumas, Romain Guyot, Alexandre Soriano, William Marande, Sandrine Arribat, Hélène Bergès, Laurence Marquès, Malika Laguerre, Thomas Blein, Erika Sallet, Davide Mancinotti, Martin Crespi, Sébastien Carrère, Matthew R. Nelson, Cecile Huneau, Jérôme Salse, Jemma Taylor, Fanchon Divol, Jean Keller, Fernando Geu-Flores, Delphine Aime, Veit Schubert, Karine Gallardo, Jérôme Gouzy, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Royal Botanic Gardens [Kew], Leibniz Institute of Plant Genetics and Crop Plant Research, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Evolution des Interactions Plantes-Microorganismes, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Copenhagen = Københavns Universitet (KU), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Royal Botanic Gardens, Kew, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Développement et Plasticité du Système Racinaire (PLASTICITE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen, Frederiksberg C, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Royal Botanic Garden , Kew, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (UNS), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 2. Zero hunger, Whole genome sequencing, 0303 health sciences, Root system, 15. Life on land, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Lupinus, Symbiosis, Arabidopsis, Botany, Cluster root, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Legume, 030304 developmental biology
Abstract: White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1–5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well asde novoassemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify theAPETALA2transcription factorLaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.
Published: 2019

10. Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field

Author: Fabrice Roux, Françoise Budar, Stéphanie Durand, Christine Camilleri, Romain Villoutreix, Marie-Laure Martin-Magniette, Tristan Mary-Huard, Lucy Botran, Elise Barillot, Estelle Wenes, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Plant Biology Department at Institut National de la Recherche Agronomique, Agence Nationale de la Recherche [ANR-12_ADAP-0004], LABEX (Laboratoire d'Excellence) [ANR-10-LABX-41, ANR-11-IDEX-0002-02], LABEX Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], Genetics and Plant Breeding Department at Institut National de la Recherche Agronomique, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR-12-ADAP-0004,CYTOPHENO,Co-adaptation nucléo-cytoplasmique et phénotypes adaptatifs des plantes(2012), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques et d'Informatique Appliquées (LAMIA), Université du Québec à Trois-Rivières (UQTR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Budar, Françoise, AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 ( Evo-Eco-Paléo ), Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Mathématiques et Informatique Appliquées ( MIA-Paris ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Institut Jean-Pierre Bourgin ( IJPB ), Institut des Sciences des Plantes de Paris-Saclay ( IPS2 ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Laboratoire des interactions plantes micro-organismes [LIPM], Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon], Laboratoire de Mathématiques et d'Informatique Appliquées [LAMIA], Mathématiques et Informatique Appliquées [MIA Paris-Saclay], Institut Jean-Pierre Bourgin [IJPB], and Institut des Sciences des Plantes de Paris-Saclay [IPS2 (UMR_9213 / UMR_1403)]
Subjects: 0301 basic medicine, Cytoplasm, Arabidopsis, Biology, Intraspecific competition, plant adaptation, 03 medical and health sciences, cytolines, cytoplasm x nucleus interactions, fitness-related traits, organelles, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Evolutionary dynamics, ComputingMilieux_MISCELLANEOUS, Cell Nucleus, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Multidisciplinary, Ecology, food and beverages, Genetic Variation, Epistasis, Genetic, Phenotypic trait, Biological Sciences, biology.organism_classification, Adaptation, Physiological, Biological Evolution, Phenotype, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], 030104 developmental biology, Evolutionary biology, Epistasis, Genetic Fitness, Adaptation, Genome, Plant
Abstract: International audience; Although the contribution of cytonuclear interactions to plant fitness variation is relatively well documented at the interspecific level, the prevalence of cytonuclear interactions at the intraspecific level remains poorly investigated. In this study, we set up a field experiment to explore the range of effects that cytonuclear interactions have on fitness-related traits in Arabidopsis thaliana. To do so, we created a unique series of 56 cytolines resulting from cytoplasmic substitutions among eight natural accessions reflecting within-species genetic diversity. An assessment of these cytolines and their parental lines scored for 28 adaptive whole-organism phenotypes showed that a large proportion of phenotypic traits (23 of 28) were affected by cytonuclear interactions. The effects of these interactions varied from slight but frequent across cytolines to strong in some specific parental pairs. Two parental pairs accounted for half of the significant pairwise interactions. In one parental pair, Ct-1/Sha, we observed symmetrical phenotypic responses between the two nuclear backgrounds when combined with specific cytoplasms, suggesting nuclear differentiation at loci involved in cytonuclear epistasis. In contrast, asymmetrical phenotypic responses were observed in another parental pair, Cvi-0/Sha. In the Cvi-0 nuclear background, fecundity and phenology-related traits were strongly affected by the Sha cytoplasm, leading to a modified reproductive strategy without penalizing total seed production. These results indicate that natural variation in cytoplasmic and nuclear genomes interact to shape integrative traits that contribute to adaptation, thereby suggesting that cytonuclear interactions can play a major role in the evolutionary dynamics of A. thaliana.
Published: 2016

11. Laser Capture Micro-Dissection Coupled to RNA Sequencing: A Powerful Approach Applied to the Model Legume Medicago truncatula in Interaction with Sinorhizobium meliloti

Author: Nathalie Rodde, Sandra Moreau, Brice Roux, Pascal Gamas, Marie-Françoise Jardinaud, Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Nobutoshi Yamaguchi, ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Sinorhizobium meliloti, biology, Polyadenylation, [SDV]Life Sciences [q-bio], RNA, Computational biology, biology.organism_classification, 01 natural sciences, Medicago truncatula, 03 medical and health sciences, 030104 developmental biology, Gene expression, RNA extraction, Transcription factor, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany, Laser capture microdissection
Abstract: Understanding the development of multicellular organisms requires the identification of regulators, notably transcription factors, and specific transcript populations associated with tissue differentiation. Laser capture microdissection (LCM) is one of the techniques that enable the analysis of distinct tissues or cells within an organ. Coupling this technique with RNA sequencing (RNAseq) makes it extremely powerful to obtain a genome-wide and dynamic view of gene expression. Moreover, RNA sequencing allows two or potentially more interacting organisms to be analyzed simultaneously. In this chapter, a LCM-RNAseq protocol optimized for root and symbiotic root nodule analysis is presented, using the model legume Medicago truncatula (in interaction with Sinorhizobium meliloti in the nodule samples). This includes the description of procedures for plant material fixation, embedding, and micro-dissection; it is followed by a presentation of techniques for RNA extraction and amplification, adapted for the simultaneous analysis of plant and bacterial cells in interaction or, more generally, polyadenylated and non-polyadenylated RNAs. Finally, step-by-step statistical analyses of RNAseq data are described. Those are critical for quality assessment of the whole procedure and for the identification of differentially expressed genes.
Published: 2018

12. A High Quality Draft Assembly of the Diploid 'Regina' Sweet Cherry Genome

Author: Le Dantec, Loick, Girollet, Nabil, Fouche, Mathieu, Gouzy, Jerome, Sallet, Erika, Quero-Garcia, José, Barreneche, Teresa, Wenden, Bénédicte, Dirlewanger, Elisabeth, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Espèces Fruitières (UREF), and Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Sweet cherry (Prunus avium L.) is a diploid species with an estimated genome size of 338 MB (Arumuganathan et al. 1991). It is mostly self-incompatible, and therefore has a heterozygous genetic background. We have sequenced and assembled the genome of the 'Regina' sweet cherry variety, which is a late blooming cultivar. Here we present a draft phased sweet cherry genome assembly using a combination of sequencing strategies (long reads sequencing with PacBio RSII and optical mapping with BioNano whole-genome maps). CONCLUSION. PacBio long reads were de novo assembled using FALCON assembler and phased using FALCON UNZIP. BioNano optical whole genome maps were used for further scaffolding. Our de novo genome assembly resulted in a genome of 279 Mb (83 % of estimated genome size), 92 scaffolds and a largest scaffold of 16,3 Mb. The assembly has high contiguity (contig N50 1,23Mb, scaffold N50 ~6Mb) and good completeness with 95,9% BUSCO genes complete (scaffolds+ unscaffolded contigs). We are now in the process of reconstructing the pseudo molecules using high density genetic linkage maps and GBS data. Structural annotation is on the way using the integrative EuGene platform with different sources of evidence available for gene prediction including transcriptomic data from Regina obtained previously in the lab (Unigene set and RNASeq).
Published: 2018

13. Whole-genome landscape of Medicago truncatula symbiotic genes

Author: David Latrasse, Christine Lelandais-Brière, William Marande, Hélène Bergès, Frédéric Debellé, Stéphane Muños, Julia Buitink, Sébastien Carrère, Andreas Niebel, Mohamed Zouine, Pascal Gamas, Jonathan Kreplak, Moussa Benhamed, Olivier Bouchez, Sandra Moreau, Marie-Françoise Jardinaud, Stéphane Cauet, Thomas Blein, Jérôme Gouzy, Carine Satgé, Erika Sallet, Yann Pecrix, Céline Lopez-Roques, Margot Zahm, Baptiste Mayjonade, Aurélie Bérard, Florian Frugier, S. Evan Staton, Martin Crespi, Abdelhafid Bendahmane, Céline Chantry-Darmon, Magali Perez, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of British Columbia, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, ANR grants EPISYM (grant no. ANR-15-CE20-0002), NODCCAAT (no. ANR-15-CE20-0012), REGULEG (no. ANR-15-CE20-0001), the ‘Laboratoire d’Excellence (LABEX)’ TULIP (no. ANR-10-LABX-41), the LABEX Saclay Plant Sciences (SPS, no. ANR-10-LABX-40) and the European Research Council (no. ERC-SEXYPARTH), and we made use of data previously generated in the ANR SYMbiMICS (ANR-08-GENO-106) and the INRA SPE EPINOD projects. The sequencing platform was supported by France Génomique National infrastructure (grant no. ANR-10-INBS-09) and by the GET-PACBIO programme (Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020)., Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-15-CE20-0002,EPISYM,Régulations épigénétiques dans le développement de nodules symbiotiques racinaires chez les légumineuses(2015), ANR-15-CE20-0012,NODCCAAT,Comprendre le mode d'action du facteur de transcription NF-YA1 spécifique de l'intearction symbiotique rhizobium-légumineuses chez Medicago truncatula(2015), ANR-15-CE20-0001,REGULEG,Identification des régulateurs participant à la plasticité d'adaptation des graines de légumineuses aux changements environnementaux(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0044,CEMAM,Center of Excellence in Multifunctional Architectured Materials(2010), ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Laboratoire des Interactions Plantes Micro organismes, Université Fédérale Toulouse Midi-Pyrénées, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), UR Etude du Polymorphisme des Génomes végétaux, Centre National de Génotypage (CNG), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Transposable element, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], RNA, Untranslated, [SDV]Life Sciences [q-bio], Symbiose, Sequence assembly, Genomics, Plant Science, Computational biology, 01 natural sciences, Genome, DNA sequencing, Epigenesis, Genetic, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Genome-wide analysis of gene expression, Gene Expression Regulation, Plant, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Gene, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Rhizobial symbiosis, Whole genome sequencing, Symbiote, Génome, biology, phytogénétique, DNA Methylation, biology.organism_classification, 030104 developmental biology, RNA, Plant, Multigene Family, Next-generation sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Root Nodules, Plant, Genome, Plant, 010606 plant biology & botany
Abstract: This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PSQE00000000.; Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.
Published: 2018

14. Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes

Author: Claudia Bartoli, Carine Huard-Chauveau, Hana Lee, Fabrice Roux, Miaoyan Wang, Dominique Roby, Mary Sara McPeek, Christopher Meyer, Joy Bergelson, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Invertebrate Zoology, Smithsonian Institution-National Museum of Natural History, Department of Ecology and Evolution [Chicago], University of Chicago, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Franco-American Fulbright Commission (Program Nord Pas de Calais), Region Midi-Pyrenees (project Accueil de nouvelles equipes d'excellence), Agence Nationale de la Recherche (ANR) projects RIPOSTE : ANR-14-CE19-0024-01, Laboratoire d'Excellence (LABEX) Towards a Unified Theory of Biotic Interactions: Role of Environmental Pertubations (TULIP) : ANR-10-LABX-41, ANR-11-IDEX-0002-02, National Institutes of Health : R01 HG001645, R01 GM083068, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Xanthomonas, Host–pathogen interaction, Quantitative Trait Loci, Arabidopsis, Genome-wide association study, Computational biology, Biology, Genome, 03 medical and health sciences, Pathosystem, Gene mapping, Genetic variation, Association mapping, ComputingMilieux_MISCELLANEOUS, Genetic association, Disease Resistance, Multidisciplinary, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Chromosome Mapping, Genetic Variation, 3. Good health, 030104 developmental biology, Phenotype, PNAS Plus, Host-Pathogen Interactions, Genome-Wide Association Study
Abstract: Infectious diseases are often affected by specific pairings of hosts and pathogens and therefore by both of their genomes. The integration of a pair of genomes into genome-wide association mapping can provide an exquisitely detailed view of the genetic landscape of complex traits. We present a statistical method, ATOMM (Analysis with a Two-Organism Mixed Model), that maps a trait of interest to a pair of genomes simultaneously; this method makes use of whole-genome sequence data for both host and pathogen organisms. ATOMM uses a two-way mixed-effect model to test for genetic associations and cross-species genetic interactions while accounting for sample structure including interactions between the genetic backgrounds of the two organisms. We demonstrate the applicability of ATOMM to a joint association study of quantitative disease resistance (QDR) in the Arabidopsis thaliana-Xanthomonas arboricola pathosystem. Our method uncovers a clear host-strain specificity in QDR and provides a powerful approach to identify genetic variants on both genomes that contribute to phenotypic variation.
Published: 2018

15. Desulfovibrio senegalensis sp. nov., a mesophilic sulfate reducer isolated from marine sediment

Author: Abdoulaye Thioye, Zouhaier Ben Ali Gam, Jean-Luc Cayol, Marc Labat, Malick Mbengue, Coumba Toure-Kane, Manon Joseph-Bartoli, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ), Université Cheikh Anta Diop ( UCAD ), and Institut de Recherche pour le Développement ( IRD )
Subjects: DNA, Bacterial, 0301 basic medicine, Geologic Sediments, 030106 microbiology, chemistry.chemical_element, Desulfovibrio senegalensis, Desulfovibrio oxyclinae, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, RNA, Ribosomal, 16S, medicine, Yeast extract, Seawater, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Thiosulfate, sulfate reducer, Base Composition, biology, Strain (chemistry), Sulfates, Fatty Acids, marine, Sequence Analysis, DNA, General Medicine, biology.organism_classification, Sulfur, Desulfovibrio, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Senegal, Halophile, Bacterial Typing Techniques, 030104 developmental biology, sediment, chemistry, Biochemistry, Oxidation-Reduction, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Bacteria
Abstract: Several strains of sulfate-reducing bacteria were isolated from marine sediments recovered from Hann Bay (Senegal). All were related to members of the genus Desulfovibrio. A strictly anaerobic, mesophilic and moderately halophilic strain designated BLaC1(T) was further characterized. Cells of strain BLaC1(T) stained Gram-negative and were 0.5 mu m wide and 2-4 mu m long, motile, rod-shaped and non-spore-forming. The four major fatty acids were anteiso-C-15 (: 0), iso-C-15 (: 0), iso-C-17 (:) (0) and anteiso-C-17 : 0. Growth was observed from 15 to 45 degrees C (optimum 40 degrees C) and at pH 5.5-8 (optimum pH 7.5). The salinity range for growth was 5-65 g NaCl l(-1) (optimum 30 g l(-1)). Yeast extract was required for growth. Strain BLaC1(T) was able to grow on lactate and acetate in the presence of sulfate as an electron acceptor. Sulfate, thiosulfate and sulfite could serve as terminal electron acceptors, but not fumarate, nitrate or elemental sulfur. The DNA G+C content was 55.8 mol%. 16S rRNA gene sequence analysis assigned strain BLaC1(T) to the family Desulfovibrionaceae; its closest relative was Desulfovibrio oxyclinae DSM 19275(T) (93.7 % similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain BLaC1(T) is proposed as representing a novel species of Desulfovibrio, with the name Desulfovibrio senegalensis sp. nov. The type strain is BLaC1(T) (=DSM 101509(T)=JCM 31063(T)).
Published: 2017

16. Cytokinins in Symbiotic Nodulation: When, Where, What For?

Author: Pascal Gamas, Mathias Brault, Florian Frugier, Marie-Françoise Jardinaud, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Ecole d'Ingénieurs de Purpan (INP - PURPAN), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), École nationale supérieure agronomique de Toulouse (ENSAT), Agence Nationale de la Recherche (ANR), Université Fédérale Toulouse Midi-Pyrénées, Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École nationale supérieure agronomique de Toulouse [ENSAT], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Université Paris Sud (Paris 11), Ecole Nationale Supérieure Agronomique de Toulouse, Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Toulouse, Institut des Sciences des Plantes de Paris-Saclay ( IPS2 ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Université Paris Diderot (Paris 7), Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ), and Ecole d'Ingénieurs de Purpan ( INPT - EI Purpan )
Subjects: 0106 biological sciences, 0301 basic medicine, Cytokinins, Organogenesis, [SDV.CAN]Life Sciences [q-bio]/Cancer, Plant Science, Root hair, Biology, Plant Root Nodulation, Plant Roots, 01 natural sciences, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 03 medical and health sciences, chemistry.chemical_compound, cytokinin, Symbiosis, Nitrogen Fixation, Botany, nodulation, cytokinine, food and beverages, Fabaceae, biology.organism_classification, Cell biology, 030104 developmental biology, chemistry, Cytokinin, Nitrogen fixation, Rhizobium, 010606 plant biology & botany
Abstract: Substantial progress has been made in the understanding of early stages of the symbiotic interaction between legume plants and rhizobium bacteria. Those include the specific recognition of symbiotic partners, the initiation of bacterial infection in root hair cells, and the inception of a specific organ in the root cortex, the nodule. Increasingly complex regulatory networks have been uncovered in which cytokinin (CK) phytohormones play essential roles in different aspects of early symbiotic stages. Intriguingly, these roles can be either positive or negative, cell autonomous or non-cell autonomous, and vary, depending on time, root tissues, and possibly legume species. Recent developments on CK symbiotic functions and interconnections with other signaling pathways during nodule initiation are the focus of this review.
Published: 2017

17. An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence

Author: Emeric Dubois, Sylvie Pagès, Anne Lanois, Julien Brillard, Maurine Bonabaud, Annabelle Mouammine, Sophie Gaudriault, Alain Givaudan, David Roche, Grégory Jubelin, Ludovic Legrand, Stéphane Cruveiller, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] ( DGIMI ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, GenomiX, Institut de Génomique Fonctionnelle, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génomique Fonctionnelle ( IGF ), Centre National de la Recherche Scientifique ( CNRS ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Montpellier 1 ( UM1 ) -Université de Montpellier ( UM ), Centre Interlangues - Texte, Image, Langage ( TIL ), Université de Bourgogne ( UB ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Sécurité et Qualité des Produits d'Origine Végétale ( SQPOV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), Ecologie microbienne des insectes et interactions hôte-pathogène ( EMIP ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), INRA 2011_1333_03 2015_1333, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Insecta, Operon, [SDV]Life Sciences [q-bio], [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, 030106 microbiology, Population, salmonella, Virulence, Drug resistance, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, peptide antimicrobien, Article, Bacterial genetics, Microbiology, 03 medical and health sciences, inhomogeneity, Disk Diffusion Antimicrobial Tests, Photorhabdus luminescens, Drug Resistance, Bacterial, Gene Order, hétérogénéité, Animals, education, ComputingMilieux_MISCELLANEOUS, photorhabdus luminescens, bactérie, education.field_of_study, Multidisciplinary, biology, Gene Expression Profiling, Enterobacteriaceae Infections, biology.organism_classification, bacterium, 030104 developmental biology, Regulon, Gene Expression Regulation, Genes, Bacterial, Mutation, Photorhabdus, Antimicrobial Cationic Peptides
Abstract: Some of the bacterial cells in isogenic populations behave differently from others. We describe here how a new type of phenotypic heterogeneity relating to resistance to cationic antimicrobial peptides (CAMPs) is determinant for the pathogenic infection process of the entomopathogenic bacterium Photorhabdus luminescens. We demonstrate that the resistant subpopulation, which accounts for only 0.5% of the wild-type population, causes septicemia in insects. Bacterial heterogeneity is driven by the PhoPQ two-component regulatory system and expression of pbgPE, an operon encoding proteins involved in lipopolysaccharide (LPS) modifications. We also report the characterization of a core regulon controlled by the DNA-binding PhoP protein, which governs virulence in P. luminescens. Comparative RNAseq analysis revealed an upregulation of marker genes for resistance, virulence and bacterial antagonism in the pre-existing resistant subpopulation, suggesting a greater ability to infect insect prey and to survive in cadavers. Finally, we suggest that the infection process of P. luminescens is based on a bet-hedging strategy to cope with the diverse environmental conditions experienced during the lifecycle.
Published: 2017
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18. Pathobiome entomopathogenic nematodes Development of methodology for a taxonomic assignation at the species level in the the pathobiome of entomopathogenic nematodes from the Steinernema genus

Author: Ogier, Jean-Claude, Gaudriault, Sophie, Heuillard, Pauline, Zemb, Olivier, Carrere, Sebastien, Galan, Maxime, Barret, Matthieu, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] ( DGIMI ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ), Institut National de la Recherche Agronomique ( INRA ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ), Centre de Biologie pour la Gestion des Populations ( CBGP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, taxonomy, amplification d'adn, activité intestinale, sol, microbiote, taxonomie, interaction microorganisme insecte, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, steinernema, écologie des populations, soil, nématode
Abstract: Pathobiome entomopathogenic nematodes Development of methodology for a taxonomic assignation at the species level in the the pathobiome of entomopathogenic nematodes from the [i]Steinernema[/i] genus . 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens)
Published: 2017

19. Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds

Author: Christine Le Signor, Julia Buitink, Valérie Labas, Jean Marie Prosperi, Delphine Aime, Jérôme Gouzy, Judith Burstin, Olivier Leprince, Karine Gallardo, Richard D. Thompson, Nevin D. Young, Amandine Bordat, Maya Belghazi, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Plant Pathology, Cornell University, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, French National Research Agency : ANR-06-GPLA-0008, ANR-09-GENM-026, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, Centre de recherche en neurobiologie - neurophysiologie de Marseille ( CRN2M ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Physiologie de la reproduction et des comportements [Nouzilly] ( PRC ), Institut National de la Recherche Agronomique ( INRA ) -Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Cornell University [New York], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Proteomics, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, protein quantity loci (PQL), Globulin, Physiology, legumes, Plant Science, Chromatin remodeling, 03 medical and health sciences, Gene Expression Regulation, Plant, Botany, Medicago truncatula, genome-wide association studies (GWAS), vegetable, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Electrophoresis, Gel, Two-Dimensional, Gene Regulatory Networks, Gene, Transcription factor, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Plant Proteins, 2. Zero hunger, Genetics, seed proteome, amélioration génétique, biology, Pisum sativum (pea), Seed Storage Proteins, Peas, food and beverages, légume, biology.organism_classification, Protein Transport, 030104 developmental biology, Vicilin, Mutation, Seeds, biology.protein, qualité des semences, semence, globulins, Genome-Wide Association Study, Transcription Factors
Abstract: AGAP : équipe GE2pop; Improving nutritional seed quality is an important challenge in grain legume breeding. However, the genes controlling the differential accumulation of globulins, which are major contributors to seed nutritional value in legumes, remain largely unknown. We combined a search for protein quantity loci with genome-wide association studies on the abundance of 7S and 11S globulins in seeds of the model legume species Medicago truncatula. Identified genomic regions and genes carrying polymorphisms linked to globulin variations were then cross-compared with pea (Pisum sativum), leading to the identification of candidate genes for the regulation of globulin abundance in this crop. Key candidates identified include genes involved in transcription, chromatin remodeling, post-translational modifications, transport and targeting of proteins to storage vacuoles. Inference of a gene coexpression network of 12 candidate transcription factors and globulin genes revealed the transcription factor ABA-insensitive 5 (ABI5) as a highly connected hub. Characterization of loss-of-function abi5 mutants in pea uncovered a role for ABI5 in controlling the relative abundance of vicilin, a sulfur-poor 7S globulin, in pea seeds. This demonstrates the feasibility of using genome-wide association studies in M. truncatula to reveal genes that can be modulated to improve seed nutritional value.
Published: 2017

20. Comparative analysis of Ralstonia solanacearum methylomes

Author: Erill, Ivan, Puigvert, Marina, Legrand, Ludovic, Guarischi-Sousa, Rodrigo, Vandecasteele, Céline, Setubal, João C., Genin, Stephane, Guidot, Alice, Valls, Marc, Department of Biological Sciences, The Open University [Milton Keynes] (OU), CSIC- IRTA- UAB -UB, Center for Research in Agricultural Genomics, Department of Genetics, The University of Texas M.D. Anderson Cancer Center [Houston], Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Spanish Ministry of Economy and Competitiveness projects : AGL2013-46898-R, AGL2016-78002-R, U.S. National Science Foundation : MCB-1158056, CERCA Program of the Catalan Government (Generalitat de Catalunya), University of Maryland, Baltimore County Office of Research, 'Severo Ochoa Program for Centers of Excellence in R&D' of the Spanish Ministry of Economy and Competitiveness, SEV-2015-0533, COST Action SUSTAIN from the European Union : FA1208, doctoral fellowship : 2012/15197-1, Sao Paulo Research Foundation (FAPESP), CNPq : 304881/2015-5, Universitat de Barcelona, France Genomique National infrastructure, as part of 'Investissement d'avenir' program, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Maryland [Baltimore County] (UMBC), University of Maryland System, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Universitat Autònoma de Barcelona (UAB), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Spanish Ministry of Economy and Competitiveness projects AGL2013-46898-RAGL2016-78002-RNational Science Foundation (NSF)MCB-1158056CERCA Program of the Catalan Government (Generalitat de Catalunya) University of Maryland Baltimore County Office of Research 'Severo Ochoa Program for Centers of Excellence in RAMP, D' of the Spanish Ministry of Economy and Competitiveness SEV-2015-0533COST Action SUSTAIN from the European Union FA1208doctoral fellowship 2012/15197-1Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) National Council for Scientific and Technological Development (CNPq)304881/2015-5Universitat de Barcelona French National Research Agency (ANR), Ministerio de Economía y Competitividad (España), National Science Foundation (US), Generalitat de Catalunya, European Commission, Sao Paulo Research Foundation, Universidad de Barcelona, Agence Nationale de la Recherche (France), The Open University [Milton Keynes] ( OU ), University of Texas M.D. Anderson Cancer Center, Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ), Universidade de São Paulo ( USP ), and Institut National de la Recherche Agronomique ( INRA )
Subjects: Epigenomics, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, comparative analysis, transposon, [SDV]Life Sciences [q-bio], Plant Science, comparative genomics, adaptation, Ralstonia, methylome, nucleotide modification, epigenomics, transcriptional, regulation, genome, Transcriptional regulation, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, plante pathogène, Phytopatogenic bacteria, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, transcriptional regulation, Bacteris fitopatògens, pathologie végétale, Transposon, Vegetal Biology, Genome, Comparative genomics, Microbiology and Parasitology, food and beverages, analyse comparative, biochemical phenomena, metabolism, and nutrition, Microbiologie et Parasitologie, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Ralstonia solanacearum, Methylome, Biologie végétale, Nucleotide modification
Abstract: Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants., This work was funded by the Spanish Ministry of Economy and Competitiveness projects AGL2013-46898-R and AGL2016-78002-R to MV and by a U.S. National Science Foundation (MCB-1158056) award to IE. We also acknowledge financial support from the CERCA Program of the Catalan Government (Generalitat de Catalunya), the University of Maryland, Baltimore County Office of Research, the “Severo Ochoa Program for Centers of Excellence in R&D” 2016–2019 (SEV-2015-0533) of the Spanish Ministry of Economy and Competitiveness and the COST Action SUSTAIN (FA1208) from the European Union. RG is the recipient of a doctoral fellowship [grant 2012/15197-1, São Paulo Research Foundation (FAPESP)]. JS has a researcher fellowship from CNPq (304881/2015-5). MP holds an APIF doctoral fellowship from Universitat de Barcelona. This work was also performed in collaboration with the GeT core facility, Toulouse, France (http://get.genotoul.fr), and was supported by France Génomique National infrastructure, funded as part of “Investissement d'avenir” program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09).
Published: 2017

21. Eggplant resistance to the Ralstonia solanacearum species complex involves both broad-spectrum and strain-specific quantitative trait loci

Author: Salgon, Sylvia, Jourda, Cyril, Sauvage, Christopher, Brand-Daunay, Marie-Christine, Reynaud, Bernard, Wicker, Emmanuel, Dintinger, Jacques, Légumière et HORticole, Association Réunionnaise pour la Modernisation de l’Economie Fruitière, Légumière et HORticole (ARMEFLHOR), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), (ANRT) through the CIFRE PhD 2013/1477, CASDAR C-2013-09, Association Réunionnaise pour la Modernisation de l’Economie Fruitière Légumière et HORticole, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Résistance génétique, Locus des caractères quantitatifs, quantitative resistance, flétrissement bactérien, plant-pathogen interaction, eggplant, mécanisme de résistance, plant–pathogen interaction, spectrum analysis, Plant Science, Relation hôte pathogène, bacterial wilt, F30 - Génétique et amélioration des plantes, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Solanum melongena, analyse spectrale, Original Research, H20 - Maladies des plantes, interaction plante pathogène, Vegetal Biology, candidate genes, résistance quantitative, candidate gene, food and beverages, Gène, plant pathogen interaction, aubergine, loci, Ralstonia solanacearum, Carte génétique, Erwinia, gène candidat, Biologie végétale
Abstract: Bacterial wilt (BW) is a major disease of solanaceous crops caused by the Ralstonia solanacearum species complex (RSSC). Strains are grouped into five phylotypes (I, IIA, IIB, III, and IV). Varietal resistance is the most sustainable strategy for managing BW. Nevertheless, breeding to improve cultivar resistance has been limited by the pathogen's extensive genetic diversity. Identifying the genetic bases of specific and non-specific resistance is a prerequisite to breed improvement. A major gene (ERs1) was previously mapped in eggplant (Solanum melongena L.) using an intraspecific population of recombinant inbred lines derived from the cross of susceptible MM738 (S) x resistant AG91-25 (R). ERs1 was originally found to control three strains from phylotype I, while being totally ineffective against a virulent strain from the same phylotype. We tested this population against four additional RSSC strains, representing phylotypes I, IIA, IIB, and III in order to clarify the action spectrum of ERs1. We recorded wilting symptoms and bacterial stem colonization under controlled artificial inoculation. We constructed a high-density genetic map of the population using single nucleotide polymorphisms (SNPs) developed from genotyping-by-sequencing and added 168 molecular markers [amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and sequence-related amplified polymorphisms (SRAPs)] developed previously. The new linkage map based on a total of 1,035 markers was anchored on eggplant, tomato, and potato genomes. Quantitative trait locus (QTL) mapping for resistance against a total of eight RSSC strains resulted in the detection of one major phylotype-specific QTL and two broad-spectrum QTLs. The major QTL, which specifically controls three phylotype I strains, was located at the bottom of chromosome 9 and corresponded to the previously identified major gene ERs1. Five candidate R-genes were underlying this QTL, with different alleles between the parents. The two other QTLs detected on chromosomes 2 and 5 were found to be associated with partial resistance to strains of phylotypes I, IIA, III and strains of phylotypes IIA and III, respectively. Markers closely linked to these three QTLs will be crucial for breeding eggplant with broad-spectrum resistance to BW. Furthermore, our study provides an important contribution to the molecular characterization of ERs1, which was initially considered to be a major resistance gene.
Published: 2017

22. Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

Author: Erika Sallet, Mireille Bétermier, Linda Sperling, Erwin van Dijk, Augustin de Vanssay, Maoussi Lhuillier-Akakpo, Olivier Arnaiz, Sandra Duharcourt, Jérôme Gouzy, Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Réarrangements programmés du génome (MICMAC), Département Biologie des Génomes (DBG), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Plateforme de séquençage à haut débit (NGS), Département Plateforme (PF I2BC), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique intramural, Agence Nationale de la Recherche Scientifique 'PIGGYPACK' : ANR-14-CE10-0005-04, INFERNO : ANR-12-BSV6-0017-03, Comite d'lle de France de la Ligue Nationale Contre le Cancer, Equipe FRM : DEQ20160334868, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Paris Sud (Paris 11), Université Paris-Saclay, Institut Jacques Monod, UMR 7592, Université Paris Diderot (Paris 7), Centre National de la Recherche Scientifique ( CNRS ), UMR 967, IRCM, Institut National de la Santé et de la Recherche Médicale ( INSERM ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), and Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Paramecium, lcsh:QH426-470, autogamy, lcsh:Biotechnology, Genomics, Computational biology, Biology, ciliate, Genome, 03 medical and health sciences, lcsh:TP248.13-248.65, Gene density, Genetics, RNA-Seq, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Differential gene expression, Paramecium aurelia, amélioration génétique, Sequence Analysis, RNA, Methodology Article, Gene Expression Profiling, Molecular Sequence Annotation, Gene Annotation, biology.organism_classification, Agricultural sciences, TSS, gene annotation, lcsh:Genetics, 030104 developmental biology, Paramecium tetraurelia, cap-Seq, Sciences agricoles, Biotechnology, Reference genome, expression des gènes
Abstract: Background The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. Results We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. Conclusions We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3′ and 5′ UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis regulatory motifs). The P. tetraurelia improved transcriptome resource, gene annotations for P. tetraurelia, P. biaurelia, P. sexaurelia and P. caudatum, and Paramecium-trained EuGene configuration are available through ParameciumDB (http://paramecium.i2bc.paris-saclay.fr). TrUC software is freely distributed under a GNU GPL v3 licence (https://github.com/oarnaiz/TrUC). Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3887-z) contains supplementary material, which is available to authorized users.
Published: 2017

23. Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development

Author: Pierre Hilson, Olga Rosspopoff, Liudmila Chelysheva, Julie Saffar, Lena Lecorgne, François Roudier, Richard Berthomé, Marco Da Costa, Delphine Gey, Vincent Colot, Erwann Caillieux, Philippe Rech, Centre National de la Recherche Scientifique (CNRS), AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA), Sorbonne Univiversité, Université Pierre et Marie Curie (Paris 6), Université Paris Diderot - Paris 7 (UPD7), UMS 2700, OMS, Muséum national d'Histoire naturelle (MNHN), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), institut de Biologie, École normale supérieure - Paris (ENS Paris), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire Interaction des Plantes Microorganismes, UMR2594, Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), project Regeneome of French Agence Nationale de la Recherche (ANR) : ANR-07-GPLA-011, Agence Nationale de la Recherche LabEx Saclay Plant Sciences-SPS : ANR-10-LABX-0040-SPS, Centre National de la Recherche Scientifique ( CNRS ), Institut Jean-Pierre Bourgin ( IJPB ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Institut National de la Recherche Agronomique ( INRA ), Université Paris Diderot, Université Paris Diderot - Paris 7 ( UPD7 ), Muséum National d’Histoire Naturelle ( MNHN ), Institut de biologie de l'ENS Paris (UMR 8197/1024) ( IBENS ), École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), École normale supérieure - Paris ( ENS Paris ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), CNRS 8114, UMR INRA 1165, Plant Genome Research Unite, UEVE, Sorbonne Université (SU), Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Plant stem cell, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Cytokinins, Time Factors, Transcription, Genetic, Cell division, transdifferentiation, Meristem, Plant Development, Biology, 03 medical and health sciences, chemistry.chemical_compound, Plant Growth Regulators, Gene Expression Regulation, Plant, Auxin, méristème racinaire, Botany, totipotency, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Primordium, stem cell niche, conversion, Molecular Biology, chemistry.chemical_classification, manipulation génétique, Gene Expression Profiling, Lateral root, fungi, Gene Expression Regulation, Developmental, food and beverages, DNA Methylation, root-to-shoot, genetic manipulation, Cell biology, arabidopsis, 030104 developmental biology, chemistry, regeneration, Cell Transdifferentiation, Shoot, Cytokinin, Cell Division, Developmental Biology
Abstract: To understand how the identity of an organ can be switched, we studied the transformation of lateral root primordia (LRP) into shoot meristems in Arabidopsis root segments. In this system, the cytokinin-induced conversion does not involve the formation of callus-like structures. Detailed analysis showed that the conversion sequence starts with a mitotic pause and is concomitant with the differential expression of regulators of root and shoot development. The conversion requires the presence of apical stem cells and only LRP at stages VI or VII can be switched. It is engaged as soon as cell divisions resume because their position and orientation differ in the converting organ compared to the undisturbed emerging LRP. By alternating auxin and cytokinin treatments, we showed that the root and shoot organogenetic programs are remarkably plastic because the status of the same plant stem cell niche can be reversed repeatedly within a set developmental window. Thus, the networks at play in the meristem of a root can morph in the span of a couple cell division cycles into those of a shoot, and back, through transdifferentiation.
Published: 2017

24. Regulation of Differentiation of Nitrogen-Fixing Bacteria by Microsymbiont Targeting of Plant Thioredoxin s1

Author: Marie M Larousse, Geneviève Alloing, Julie Hopkins, Pierre P Frendo, Sofiane Sm Benyamina, Jérémy Couturier, Pascal Gamas, Nicolas Rouhier, Claude Castella, Fabien Baldacci-Cresp, Olivier Pierre, Françoise Montrichard, Annie Lambert, Carolina Werner Cw Ribeiro, Julie Cazareth, Peter Mergaert, Eric Boncompagni, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Institut de pharmacologie moléculaire et cellulaire (IPMC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Brazil), French Ministere de l'Enseignement Superieur et de la Recherche, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, University of Nice-Sophia Antipolis, French Government (Agence Nationale de la Recherche [ANR]) : ANR-11-LABX-0028-01 ANR, Investissements d'Avenir program, ANR-11-LABX-0002-01, ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, ANR: 11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut Sophia Agrobiotech [Sophia Antipolis] ( ISA ), Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut National de la Recherche Agronomique ( INRA ), Institut de pharmacologie moléculaire et cellulaire ( IPMC ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Intéractions Plantes-Bactéries ( PBI ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, and ANR : LABEX SIGNALIFE,ANR-11-LABX-0028-01
Subjects: 0106 biological sciences, 0301 basic medicine, Nitrogen-Fixing Bacteria, animal structures, [SDV]Life Sciences [q-bio], nodule cysteine-rich peptides, 01 natural sciences, bacteroids, General Biochemistry, Genetics and Molecular Biology, thioredoxins, Rhizobia, disulfide bond reduction, nitrogen-fixing symbiosis, 03 medical and health sciences, Gene Expression Regulation, Plant, Medicago truncatula, Gene silencing, Endoreduplication, Cysteine, Symbiosis, Gene, Sinorhizobium meliloti, [ SDV ] Life Sciences [q-bio], biology, food and beverages, differentiation, biology.organism_classification, Peptide Fragments, 030104 developmental biology, Biochemistry, redox state, thiol modifications, Ectopic expression, Thioredoxin, General Agricultural and Biological Sciences, Root Nodules, Plant, 010606 plant biology & botany, Signal Transduction
Abstract: International audience; Legumes associate with rhizobia to form nitrogen (N2)-fixing nodules, which is important for plant fitness [1, 2]. Medicago truncatula controls the terminal differentiation of Sinorhizobium meliloti into N2-fixing bacteroids by producing defensin-like nodule-specific cysteine-rich peptides (NCRs) [3, 4]. The redox state of NCRs influences some biological activities in free-living bacteria, but the relevance of redox regulation of NCRs in planta is unknown [5, 6], although redox regulation plays a crucial role in symbiotic nitrogen fixation [7, 8]. Two thioredoxins (Trx), Trx s1 and s2, define a new type of Trx and are expressed principally in nodules [9]. Here, we show that there are four Trx s genes, two of which, Trx s1 and s3, are induced in the nodule infection zone where bacterial differentiation occurs. Trx s1 is targeted to the symbiosomes, the N2-fixing organelles. Trx s1 interacted with NCR247 and NCR335 and increased the cytotoxic effect of NCR335 in S. meliloti. We show that Trx s silencing impairs bacteroid growth and endoreduplication, two features of terminal bacteroid differentiation, and that the ectopic expression of Trx s1 in S. meliloti partially complements the silencing phenotype. Thus, our findings show that Trx s1 is targeted to the bacterial endosymbiont, where it controls NCR activity and bacteroid terminal differentiation. Similarly, Trxs are critical for the activation of defensins produced against infectious microbes in mammalian hosts. Therefore, our results suggest the Trx-mediated regulation of host peptides as a conserved mechanism among symbiotic and pathogenic interactions.
Published: 2016

25. Identification de gènes liés à la résistance aux herbicides non liée à la cible chez les Ivraies : vers des tests « moléculaires » de diagnostic

Author: Délye, Christophe, Duhoux, Arnaud, Carrere, Sebastien, Bonin, Ludovic, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), ARVALIS - Institut du végétal [Paris], Association Française de Protection des Plantes (AFPP). FRA., Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), ProdInra, Archive Ouverte, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), and ARVALIS - Institut du Végétal
Subjects: [SDV] Life Sciences [q-bio], PCR, [ SDV ] Life Sciences [q-bio], rye-grass, [SDV]Life Sciences [q-bio], detection, ivraie, ALS, non-target-site-based resistance, résistance non liée à la cible
Abstract: Identification of genes linked to non-target-site resistance to herbicides in ryegrass : towards "molecular" diagnosis assays. Setting up molecular diagnosis tools would greatly foster preventing and managing non-target-sitebased resistance to herbicides (NTSR). This is currently hampered by the complexity of NTSR genetic determinism, which is largely based upon differences in the expression of an unknown number of genes between resistant and sensitive plants. Identifying NTSR genes is thus a challenging task. Herein, we report the identification of 19 genes which expression patterns are correlated to NTSR to ALS-inhibiting herbicides in rye-grasses (Lolium sp.). We demonstrate the potential of using combined expression data from several of these genes to predict NTSR, Le développement de tests moléculaires de détection serait un grand pas en avant dans la prévention et la gestion de la résistance non liée à la cible (RNLC). Les déterminismes génétiques de la RNLC sont cependant complexes, et font largement appel à des différences d’expression d’un nombre inconnu de gènes entre plantes résistantes et plantes sensibles. Leur identification est donc ardue. Dans ce travail, nous décrivons l’identification de 19 gènes dont les profils d’expression sont corrélés à la RNLC à des herbicides inhibiteurs de l’ALS chez les Ivraies (Lolium sp.), et nous montrons le potentiel de l’utilisation des données d’expression combinées de plusieurs de ces gènes pour la prédiction de la RNLC.
Published: 2016

26. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Author: BADOUIN, Hélène, Gouzy, Jerome, GRASSA, Christopher, Murat, Florent, Staton, S Evan, Cottret, Ludovic, Lelandais-briere, Christine, Owens, Gregory L, Carrere, Sebastien, mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C, Bowers, John E, Hubner, Sariel, Bellec, Arnaud, Berard, Aurélie, Berges, Helene, BLANCHET, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Cecile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J, Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, LORENZON, Lolita, Mandel, Jennifer R, Marage, Gwenola, MARCHAND, Gwenaëlle, MARQUAND, Elodie, MESTRIES, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot - Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Céline, Vares, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M, Salse, Jerome, Munos, Stephane, Vincourt, Patrick, Rieseberg, Loren H, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Botany and Biodiversity Research Centre, University of British Columbia (UBC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Department of Plant Biology, Miller Plant Sciences, University of Georgia [USA], Department of Biotechnology, Tel-Hai Academic College, Galilee Research Institute (Migal), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Dow AgroSciences LLC, Biogemma, GeT PlaGe, Genotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Department of Plant Sciences, University of California, Department of Biology, Northern Arizona University [Flagstaff], Center for Genomics and Bioinformatics, Indiana University [Bloomington], Indiana University System-Indiana University System, Department of Biological Sciences, The Open University [Milton Keynes] (OU), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Department of Horticulture, University of Wisconsin-Madison, The Wellcome Trust Sanger Institute [Cambridge], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), French National Research Agency : SUNYFUEL/ANR-07-GPLA-0022, SUNRISE/ANR-11-BTBR-0005 Midi-Pyrenees Region, European Fund for Regional Development, French Fund for Competitiveness Clusters (FUI), Genoscope SystemSun project, Genome Canada, Genome BC's Applied Genomics Research in Bioproducts or Crops (ABC) Competition, NSF Plant Genome Program : DBI-082045, International Consortium for Sunflower Genomics Resources, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Tel-Hai College, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-07-GPLA-0022,SUNYFUEL,Improving sunflower yield and quality for biofuel production by genomics and genetics(2007), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Galilee Research Institute [Israël] (MIGAL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of California (UC), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), University of British Columbia ( UBC ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut National de la Recherche Agronomique ( INRA ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Department of Ecology and Evolutionary Biology ( Faculty of Biology ), University of Georgia, Galilee Research Institute ( Migal ), Centre National de Ressources Génomiques Végétales ( CNRGV ), Institut National de la Recherche Agronomique ( INRA ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, The Open University [Milton Keynes] ( OU ), University of Wisconsin-Madison [Madison], Wellcome Trust Sanger Institute, and Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA )
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, sunflower, Acclimatization, résistance au stress, génome végétal, Flowers, genome evolution, résilience, Evolution, Molecular, Gene Expression Regulation, Plant, Stress, Physiological, Gene Duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Oils, Sunflower Oil, genome, food and beverages, Genetic Variation, Genomics, Sequence Analysis, DNA, tournesol, genêtic variation, stress biotique, diversité génétique, Helianthus, Transcriptome, Genome, Plant
Abstract: The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.
Published: 2016

27. The type III effector RipAX2 confers avirulence of #Ralstonia solanacearum# to the eggplant AG91-25, carrying the resistance gene Ers1

Author: Guinard, Jérémy, WANG, Keke, Lonjon, Fabien, Sujeeun, Lakshmi, Mechan Llontop, Marco E., Cazalé, Anne-Claire, Barberis, Patrick, Genin, Stéphane, DAUNAY, Marie-Christine, Dintinger, Jacques, Poussier, Stéphane, Vinatzer, Boris A., Peeters, Nemo, Wicker, Emmanuel, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Univ, Réunion, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Unité de recherche Génétique et amélioration des fruits et légumes (GALF)
Subjects: [SDV] Life Sciences [q-bio], Vegetal Biology, [SDV]Life Sciences [q-bio], solanum melongena, solanum torvum, Ralstonia solanacearum, Sciences du vivant, gène de résistance, Sciences agricoles, ComputingMilieux_MISCELLANEOUS, Biologie végétale, Agricultural sciences, H20 - Maladies des plantes
Abstract: International audience; no abstract
Published: 2016

28. Functional assignment to positively selected sites in the core type III effector RipG7 from \textitR \textitalstonia solanacearum: RipG7 evolution, structure/function

Author: Chiu-Ping Cheng, Maria Anisimova, Chien-Hui Li, Fabien Lonjon, Stéphane Genin, Ilona Kars, Fabienne Vailleau, Andrey V. Kajava, Nemo Peeters, Philippe Remigi, Keke Wang, Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Computer Science [ETH Zürich] (D-INFK), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Centre National de la Recherche Scientifique (CNRS), Centre de recherches de biochimie macromoléculaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-IFR122-Centre National de la Recherche Scientifique (CNRS), National Taiwan University [Taiwan] (NTU), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), and LABEX 'TULIP' ANR-10-LABX-41 COST Action SUSTAIN FA1208 China Scholarship Council ANR-07-JCJC-0133
Subjects: 0301 basic medicine, virulence fonction, LRR, Soil Science, Virulence, ralstonia solanacearum, Plant Science, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Type three secretion system, 03 medical and health sciences, Phylogenetics, positive selection, Botany, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Genetics, Ralstonia solanacearum, biology, Effector, fungi, food and beverages, medicago truncatula, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Medicago truncatula, Plant disease, Complementation, 030104 developmental biology, Agronomy and Crop Science, type III effector
Abstract: article présenté lors du congrès Plant Biology 2015 ; Minneapolis (Etats-Unis) - (2015-07-26 - 2015-07-30); International audience; The soil-borne pathogen Ralstonia solanacearum causes bacterial wilt in a broad range of plants. The main virulence determinants of R. solanacearum are the type III secretion system (T3SS) and its associated type III effectors (T3Es), translocated into the host cells. Of the conserved T3Es among R. solanacearum strains, the Fbox protein RipG7 is required for R. solanacearum pathogenesis on Medicago truncatula. In this work, we describe the natural ripG7 variability existing in the R. solanacearum species complex. We show that eight representative ripG7 orthologues have different contributions to pathogenicity on M. truncatula: only ripG7 from Asian or African strains can complement the absence of ripG7 in GMI1000 (Asian reference strain). Nonetheless, RipG7 proteins from American and Indonesian strains can still interact with M. truncatula SKP1-like/MSKa protein, essential for the function of RipG7 in virulence. This indicates that the absence of complementation is most likely a result of the variability in the leucine-rich repeat (LRR) domain of RipG7. We identified 11 sites under positive selection in the LRR domains of RipG7. By studying the functional impact of these 11 sites, we show the contribution of five positively selected sites for the function of RipG7CMR15 in M. truncatula colonization.This work reveals the genetic and functional variation of the essential core T3E RipG7 from R. solanacearum.This analysis is the first of its kind on an essential disease-controlling T3E, and sheds light on the co-evolutionary arms race between the bacterium and its hosts.
Published: 2016

29. Quantitative disease resistance to the bacterial pathogen X anthomonas campestris involves an Arabidopsis immune receptor pair and a gene of unknown function

Author: Debieu, Marilyne, Huard-Chauveau, Carine, Genissel, Anne, ROUX, Fabrice, Roby, Dominique, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), French Agence Nationale de la Recherche-ANR blanc grant ANR-09-BLAN-0072 French Laboratory of Excellence project 'TULIP' ANR-10-LABX-41 ANR-11-IDEX-0002-02, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Arabidopsis thaliana, Arabidopsis Proteins, Quantitative Trait Loci, Arabidopsis, Receptors, Cell Surface, Original Articles, mutant analysis, Genes, Plant, Xanthomonas campestris, quantitative disease resistance, Mutation, RRS1/RPS4, GWA mapping, ComputingMilieux_MISCELLANEOUS, Disease Resistance, Plant Diseases, Plant Proteins
Abstract: Although quantitative disease resistance (QDR) is a durable and broad‐spectrum form of resistance in plants, the identification of the genes underlying QDR is still in its infancy. RKS 1 (Resistance related K ina S e1) has been reported recently to confer QDR in A rabidopsis thaliana to most but not all races of the bacterial pathogen X anthomonas campestris pv. campestris (X cc). We therefore explored the genetic bases of QDR in A . thaliana to diverse races of X . campestris (X c). A nested genome‐wide association mapping approach was used to finely map the genomic regions associated with QDR to X cc12824 (race 2) and X cc CFBP 6943 (race 6). To identify the gene(s) implicated in QDR, insertional mutants (T‐DNA) were selected for the candidate genes and phenotyped in response to X c. We identified two major QTLs that confer resistance specifically to Xcc12824 and XccCFBP6943. Although QDR to X cc12824 is conferred by At5g22540 encoding for a protein of unknown function, QDR to X cc CFBP 6943 involves the well‐known immune receptor pair RRS1/RPS4. In addition to RKS 1, this study reveals that three genes are involved in resistance to X c with strikingly different ranges of specificity, suggesting that QDR to X c involves a complex network integrating multiple response pathways triggered by distinct pathogen molecular determinants.
Published: 2016

30. Un ensemble coordonné de plateformes ouvertes la recherche internationale en écotoxicologie : Analyse et Expérimentation sur les Ecosystèmes – France

Author: Mougin, Christian, Azam, Didier, Caquet, Thierry, Cheviron, Nathalie, Dequiedt, Samuel, Le Galliard, Jean-François, Guillaume, Olivier, Houot, Sabine, Lacroix, Gérard, Lafolie, Francois, Maron, Pierre-Alain, Michniewicz, Radika, Pichot, Christian, Ranjard, Lionel, Roy, Jacques, Zeller, Bernhard, Clobert, Jean, Chanzy, Andre, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité d'Ecologie et Ecotoxicologie Aquatiques (UEEA), Institut National de la Recherche Agronomique (INRA), Département Ecologie des Forêts, Prairies et milieux Aquatiques (DEPT EFPA), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Ecologie des Forêts Méditerranéennes (URFM), Écotron Européen de Montpellier, Centre National de la Recherche Scientifique (CNRS), Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Station d'écologie théorique et expérimentale (SETE), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes ( ECOSYS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Unité d'Ecologie et Ecotoxicologie Aquatiques ( UEEA ), Institut National de la Recherche Agronomique ( INRA ), Département Ecologie des Forêts, Prairies et milieux Aquatiques ( DEPT EFPA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut d'écologie et des sciences de l'environnement de Paris ( IEES ), Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes ( EMMAH ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), Université Paul Sabatier - Toulouse 3 ( UPS ), Ecologie des Forêts Méditerranéennes ( URFM 629 ), UPS 3248, Écotron Européen de Montpellier - Baillarguet, Centre National de la Recherche Scientifique ( CNRS ), Interactions Sol Plante Atmosphère ( ISPA ), Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine ( Bordeaux Sciences Agro ), CNRS, Centre National de la Recherche Scientifique - MNHN - CNRS - USR 2936, Station d’Ecologie Expérimentale, Moulis, France, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées, Ecologie des Forêts Méditerranéennes [Avignon] (URFM 629), Écotron Européen de Montpellier - UPS 3248, Interactions Sol Plante Atmosphère (ISPA), Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: Un ensemble coordonné de plateformes ouvertes la recherche internationale en écotoxicologie : Analyse et Expérimentation sur les Ecosystèmes – France. Colloque « Construire le réseau ANTIOPES 2.0 - La toxicologie et l’écotoxicologie prédictives : de l’appliqué à l’opérationnel »
Published: 2016

31. Editorial: genomics and effectomics of the crop killer Xanthomonas

Author: Nicolas Denancé, Thomas Lahaye, Laurent D. Noël, Denance, Nicolas, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Zentrum für Molekularbiologie der Pflanzen ( ZMBP ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), and Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0301 basic medicine, Xanthomonas, [SDV]Life Sciences [q-bio], Plant Immunity, Virulence, chemical and pharmacologic phenomena, Plant Science, Biology, Plant disease resistance, lcsh:Plant culture, susceptibility, Crop, resistance, 03 medical and health sciences, TAL effector, Type III effectors, transcription activator like (TAL) effector, xop, medicine, crop, lcsh:SB1-1110, 2. Zero hunger, Genetics, Comparative genomics, Canker, [ SDV ] Life Sciences [q-bio], business.industry, fungi, food and beverages, Genomics, 15. Life on land, medicine.disease, biology.organism_classification, immunity, Biotechnology, type III effector, 030104 developmental biology, business
Abstract: Phytopathogenic bacteria of the Xanthomonas genus cause severe diseases on hundreds of host plants, including economically important crops, such as bean, cabbage, cassava, citrus, hemp, pepper, rice, sugarcane, tomato, or wheat. Diseases occurring in nature comprise bacterial blight, canker, necrosis, rot, scald, spot, streak, or wilt. Xanthomonas spp., are distributed worldwide, and pathogenic and non-pathogenic strains are essentially found in association to plants. Some phytopathogenic strains are emergent or re-emergent and, consequently, dramatically impact agriculture, economy, and food safety. During the last decades, massive efforts were undertaken to decipher Xanthomonas biology. So far, more than 100 complete or draft genomes from diverse Xanthomonas species have been sequenced (http://www.xanthomonas.org), thus providing powerful tools to study genetic determinants triggering pathogenicity and adaptation to plant habitats. Xanthomonas spp., employ an arsenal of virulence factors to invade its host, including extracellular polysaccharides, plant cell wall-degrading enzymes, adhesins, and secreted effectors. In most xanthomonads, type III secretion (T3S) system and secreted effectors (T3Es) are essential to bacterial pathogenicity through the inhibition of plant immunity or the induction of plant susceptibility (S) genes, as reported for Transcription Activation-Like (TAL) effectors. Yet, toxins can also be major virulence determinants in some xanthomonads while non-pathogenic Xanthomonas species do live in sympatry with plant without any T3S systems nor T3Es. In a context of ever increasing international commercial exchanges and modifications of the climate, monitoring and regulating pathogens spread is of crucial importance for food security. A deep knowledge of the genomic diversity of Xanthomonas spp., is required for scientists to properly identify strains, to help preventing future disease outbreaks and to achieve knowledge-informed sustainable disease resistance in crops. This research topic published in the “Plant Biotic Interactions” section of Frontiers in Plant Science and Frontiers in Microbiology aims at illustrating several of the recent achievements of the Xanthomonas community. We collected twelve manuscripts dealing with comparative genomics or T3E repertoires, including five focusing on TAL effectors which we hope will contribute to advance research on plant pathogenic bacteria.
Published: 2016

32. Diversity and Mechanisms of Genomic Adaptation in Penicillium

Author: Jeanne Ropars, Ricardo Rodriguez de la Vega, Manuela López-Villavicencio, Jerome Gouzy, Joëlle Dupont, Dominique Swennen, Emilie Dumas, Tatiana Giraud, Antoine Branca, Université Paris-Sud - Paris 11 (UP11), Centre National de la Recherche Scientifique (CNRS), Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AgroParisTech, Univ. Paris-Sud, Université Paris-Saclay, Ronald P. de Vries, Isabelle Benoit Gelber, Mikael Rørdam Andersen, European Project: 309403,EC:FP7:ERC,ERC-2012-StG_20111109,GENOMEFUN(2013), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 2. Zero hunger, 0303 health sciences, 03 medical and health sciences, 030306 microbiology, [SDV]Life Sciences [q-bio], food and beverages, 15. Life on land, 030304 developmental biology
Abstract: International audience; Penicillium is a diverse fungal genus with hundreds of species occurring worldwide in various substrates, from soil to food, and with various lifestyles, from necrotrophic pathogenicity to endophytic mutualism. Several species are important for human affairs, being widely used in industry, such as the penicillin-producer P. rubens, the two cheese starters P. camemberti and P. roqueforti, and the mould used for fermenting sausages, P. nalgiovense. Other species are food spoilers that produce harmful mycotoxins or cause damages in fruit crops. Currently , 30 genomes of Penicillium belonging to 18 species are available. In this chapter, we reconstruct a phylogenetic tree based on available Penicillium genomes and outline the main features of the genomes, such as gene and transposable element content. We then review the recent advances that the available genomic and transcriptomic resources in the Penicillium genus have allowed regarding our understanding of the genomic processes of adaptation, including changes in gene content, expression and strikingly frequent and recent horizontal gene transfers. In addition, we summarize recent studies using genetic markers on the level of genetic diversity, mode of reproduction and population structure within Penicillium species. Overall, the Penicillium genus appears a highly suitable model for studying the mechanisms of adaptation. Introduction Penicillium is a diverse fungal genus with 354 accepted species today (Visagie et al., 2014b), occurring worldwide in various substrates, from soil to food. Their lifestyles also cover a broad range, from necrotrophic pathogenicity to endophytic mutualism, although most are saprotrophs. As a consequence of these ecological niches, many Penicillium species have important economic and social relevance for human populations. Several species are widely used in industry, such as the penicillin-producer P. rubens, the two cheese starters P. camem-berti and P. roqueforti, and the mould used for fermenting sausages, P. nalgiovense (Bernáldez et al., 2013). Other species cause damages and yield loss in fruit crops, e.g. P. digitatum and P. italicum, while others are a concern for food safety because of their production of myco-toxins, such as patulin (Eckert and Eaks, 1989; McCallum et al., 2002).
Published: 2016

33. Ectopic expression of a Meloidogyne incognita dorsal gland protein in tobacco accelerates the formation of the nematode feeding site

Author: M. F. GROSSI-de-SÁ, Thales L. Rocha, Aulus E. A. D. Barbosa, Diva Maria de Alencar Dusi, Djair S.L. Souza, Eduardo Romano, Janice de Almeida-Engler, Cezar Martins-de-Sa, Bruna Araujo De Sousa, Regina M. D. G. Carneiro, Natália Faustino Pires, Erich Y.T. Nakasu, G. R. Oliveira, José Dijair Antonino de Souza, Maria Fatima Grossi-de-Sa, Gilbert Engler, Rodrigo da Rocha Fragoso, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Universidade de Brasília (UnB), Universidade Católica de Brasília (UCB), Universidade Federal do Rio Grande do Sul (UFRGS), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), CNPq, CAPES, FAP-DF, Embrapa Genetic Resources and Biotechnology (Brazil), and INRA (France)
Subjects: 0106 biological sciences, Time Factors, [SDV]Life Sciences [q-bio], Gene Expression, ELEGANS, Plant Science, Plant Roots, 01 natural sciences, Ectopic protein expression, Nematode's life cycle, CLAVATA3, Meloidogyne incognita, Gall, 2. Zero hunger, 0303 health sciences, biology, food and beverages, Helminth Proteins, General Medicine, Plants, Genetically Modified, Cell biology, Phenotype, Female, Terra incognita, Parasitic infection, DNA, Complementary, GENES, Recombinant Fusion Proteins, Green Fluorescent Proteins, HETERODERA-GLYCINES, Host-Parasite Interactions, Cell wall, 03 medical and health sciences, RNAI, Tobacco, Botany, Genetics, medicine, Animals, Root-knot nematode, RNA, Messenger, Tylenchoidea, Parasite Egg Count, Plant Diseases, 030304 developmental biology, medicine.disease, biology.organism_classification, PLANT-PARASITIC NEMATODE, Nematode, Nematode infection, CELLS, ARABIDOPSIS-THALIANA, Ectopic expression, LIGAND, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Meloidogyne spp., plant-parasitic nematodes present worldwide, are intensively studied because of the damage caused to a large variety of agronomically important crops. Several reports indicate that proteins from the Meloidogyne spp. dorsal gland might play an important role to allow proper establishment of a functional nematode feeding site. The precise role of these proteins in the process of feeding cell development is unknown. To gain insights into the function of these secreted M. incognita proteins, we constitutively (ectopically) expressed the nematodes dorsal gland protein 7E12 in tobacco plants. It was found that the number of galls at 8 and 16 days after nematode infection was significantly higher in transgenic plants compared to control plants. Eggs from nematodes in transgenic plants hatched faster than those in control plants. Histological analysis of nematode induced galls in transgenic plants clearly shows a different morphology. Giant feeding cells harbor more vacuoles and an increased amount of cell wall invaginations, while neighboring cells surrounding feeding cells are more numerous. These results suggest that the presence of the 7E12 protein in tobacco accelerates gall formation. This assumption is supported by our data illustrating faster gall formation and egg eclosion in transgenic plants. (C) 2010 Elsevier Ireland Ltd. All rights reserved.
Published: 2011

34. Oxytocin Controls Differentiation of Human Mesenchymal Stem Cells and Reverses Osteoporosis

Author: Ez-Zoubir Amri, Emmanuel Lemichez, Claude Laurent Benhamou, Liana Euller-Ziegler, Georges F. Carle, Armelle Basillais, Véronique Breuil, Laure-Emmanuelle Zaragosi, Christian Elabd, Zlatko Trajanoski, Florence Massiera, H. Beaupied, Marcel Scheideler, Christian Dani, Nicole Wagner, Gérard Ailhaud, Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Biomécanique et génie biomédical (BIM), Centre National de la Recherche Scientifique (CNRS), Service de rhumatologie, Centre Hospitalier Universitaire de Nice (CHU Nice)-Hôpital l'Archet, Génétique, physiopathologie et ingénierie du tissu osseux (GéPITOS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Toxines bactériennes dans la relation hôtes-pathogènes, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Génétique et signalisation moléculaire (GSM), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre Hospitalier Universitaire de Nice (CHU Nice)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Caractérisation du tissu osseux par imagerie : techniques et applications, Université d'Orléans (UO)-Centre Hospitalier Régional d'Orléans (CHRO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional d'Orléan (CHRO), Institut de Prévention et de Recherches sur l'ostéoporose, Dynamique cellulaire et moléculaire de la muqueuse respiratoire, Université de Reims Champagne-Ardenne (URCA)-IFR53-Institut National de la Santé et de la Recherche Médicale (INSERM), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Dysfonctions métaboliques et diabètes: Mécanismes et approches thérapeutiques, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Genomics and Bioinformatics, Graz, Karl-Franzens-Universität [Graz, Autriche], Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR50-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre Hospitalier Universitaire de Nice (CHU Nice)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université d'Orléans (UO)-Centre Hospitalier Régional d'Orléans (CHR)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA)
Subjects: Male, medicine.medical_specialty, Ovariectomy, Osteoporosis, Osteoclasts, Bone Marrow Cells, 030209 endocrinology & metabolism, Biology, Oxytocin, Bone resorption, Bone remodeling, Mice, 03 medical and health sciences, 0302 clinical medicine, Osteogenesis, Internal medicine, medicine, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Cells, Cultured, Osteoporosis, Postmenopausal, Aged, 030304 developmental biology, Aged, 80 and over, 0303 health sciences, Adipogenesis, Osteoblasts, Mesenchymal stem cell, Mesenchymal Stem Cells, Osteoblast, Cell Biology, Middle Aged, medicine.disease, Rats, 3. Good health, medicine.anatomical_structure, Endocrinology, Receptors, Oxytocin, Child, Preschool, Ovariectomized rat, Molecular Medicine, Female, Bone marrow, Developmental Biology
Abstract: Osteoporosis constitutes a major worldwide public health burden characterized by enhanced skeletal fragility. Bone metabolism is the combination of bone resorption by osteoclasts and bone formation by osteoblasts. While increase in bone resorption is considered as the main contributor of bone loss that may lead to osteoporosis, this loss is accompanied by increased bone marrow adiposity. Osteoblasts and adipocytes share the same precursor cell and an inverse relationship exists between the two lineages. Therefore, identifying signaling pathways that stimulates mesenchymal stem cells osteogenesis at the expense of adipogenesis is of major importance in order to develop new therapeutic treatments. For this purpose, we identified by transcriptomic analysis the oxytocin receptor pathway as a potential regulator of the osteoblast/adipocyte balance of human multipotent adipose-derived stem (hMADS) cells. Both oxytocin (OT) and carbetocin (Cb, a stable OT analogue) negatively modulate adipogenesis while promoting osteogenesis in both hMADS cells and human bone marrow mesenchymal stromal cells (hBMSC). Consistent with these observations ovariectomized (OVX) mice and rats, which become osteoporotic and exhibit disequilibrium of this balance, have significant decreased OT levels compared to sham-operated controls. Subcutaneous OT injection reverses bone loss in OVX mice and reduces marrow adiposity. Clinically, plasma OT levels are significantly lower in postmenopausal women developing osteoporosis than in their healthy counterparts. Taken together, these results suggest that plasma OT levels represent a novel diagnostic marker for osteoporosis and that OT administration holds promise as a potential therapy for this disease. ______________________________________________________________________________ Author contributions: C.E.: carried out most of the experiments, data analysis and interpretation, collection and assembly of data; A.B., H.B. and C.B.: analysis of bone micro-architecture and biomechanical parameters of mice, manuscript writing; L.Z., M.S. and Z.T.: microarray analysis, data analysis and interpretation; F.M.: contribution to the mice study, data analysis and interpretation; V.B., G.F.C. and L.E.: provision of patients, data analysis and interpretation; N.W.: histological analysis of mice tissues, data analysis and interpretation; E.L.: provision of study material, data analysis and interpretation; C.D.: data analysis and interpretation, manuscript writing; G.A.: conception and design, data analysis and interpretation, manuscript writing; E.A.: conception and design, collection and assembly of data, data analysis and interpretation, manuscript writing.
Published: 2008

35. Distinct Dynamics of HISTONE3 Variants between the Two Fertilization Products in Plants

Author: Tetsuya Higashiyama, Frédéric Berger, Yuki Hamamura, Mathieu Gourgues, Mathieu Ingouff, National University of Singapore (NUS), The University of Tokyo (UTokyo), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), and Nagoya University
Subjects: 0106 biological sciences, Arabidopsis, ENDOSPERM, DEVBIO, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, HISTONE3, Biology, Genes, Plant, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Endosperm, Histones, 03 medical and health sciences, ZYGOTE, Gene Expression Regulation, Plant, GENOMIC IMPRINTING, H3 VARIANTS, Epigenetics, Crosses, Genetic, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Zygote, Agricultural and Biological Sciences(all), Arabidopsis Proteins, Biochemistry, Genetics and Molecular Biology(all), Reproduction, Genetic Variation, ARABIDOPSIS THALIANA, food and beverages, Chromatin Assembly and Disassembly, Chromatin, Sexual reproduction, Histone, DNA methylation, biology.protein, General Agricultural and Biological Sciences, Reprogramming, FERTILIZATION PROCESS, 010606 plant biology & botany
Abstract: SummarySexual reproduction involves epigenetic reprogramming [1] comprising DNA methylation [2] and histone modifications [3–6]. In addition, dynamics of HISTONE3 (H3) variant H3.3 upon fertilization are conserved in animals, suggesting an essential role [7–9]. In contrast to H3, H3.3 marks actively transcribed regions of the genome and can be deposited in a replication-independent manner [10, 11]. Although H3 variants are conserved in plants, their dynamics during fertilization have remained unexplored. We overcame technical limitations to live imaging of the fertilization process in Arabidopsis thaliana and studied dynamics of the male-gamete-specific H3.3 [12] and the centromeric Histone Three Related 12 (HTR12) [13]. The double-fertilization process in plants produces the zygote and the embryo-nourishing endosperm [14]. We show that the zygote is characterized by replication-independent removal of paternal H3.3 and homogeneous incorporation of parental chromatin complements. In the endosperm, the paternal H3.3 is passively diluted by replication while the paternal chromatin remains segregated apart from the maternal chromatin (gonomery). Hence epigenetic regulations distinguish the two products of fertilization in plants. H3.3-replication-independent dynamics and gonomery also mark the first zygotic divisions in animal species [5, 15]. We thus propose the convergent selection of parental epigenetic imbalance involving H3 variants in sexually reproducing organisms.
Published: 2007

36. Nitrogen Fixation Control under Drought Stress. Localized or Systemic?

Author: Daniel Marino, Pierre Frendo, Ruben Ladrera, Ana Zabalza, Alain Puppo, Cesar Arrese-Igor, Esther M. González, Universidad de Navarra [Pamplona] (UNAV), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Physiology, Gene Expression, NITROGEN FIXATION, Plant Science, 01 natural sciences, Disasters, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genetics, Symbiosis, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, food and beverages, Water, Fabaceae, Isocitrate Dehydrogenase, Plant Leaves, CELL REDOX IMBALANCE, LOCAL LEVEL CONTROL, PISUM SATIVUM, DROUGHT STRESS, Oxidation-Reduction, Rhizobium, Research Article, 010606 plant biology & botany
Abstract: Legume-Rhizobium nitrogen fixation is dramatically affected under drought and other environmental constraints. However, it has yet to be established as to whether such regulation of nitrogen fixation is only exerted at the whole-plant level (e.g. by a systemic nitrogen feedback mechanism) or can also occur at a local nodule level. To address this question, nodulated pea (Pisum sativum) plants were grown in a split-root system, which allowed for half of the root system to be irrigated at field capacity, while the other half was water deprived, thus provoking changes in the nodule water potential. Nitrogen fixation only declined in the water-deprived, half-root system and this result was correlated with modifications in the activities of key nodule's enzymes such as sucrose synthase and isocitrate dehydrogenase and in nodular malate content. Furthermore, the decline in nodule water potential resulted in a cell redox imbalance. The results also indicate that systemic nitrogen feedback signaling was not operating in these water-stressed plants, since nitrogen fixation activity was maintained at control values in the watered half of the split-root plants. Thus, the use of a partially draughted split-root system provides evidence that nitrogen fixation activity under drought stress is mainly controlled at the local level rather than by a systemic nitrogen signal. © 2007 American Society of Plant Biologists.
Published: 2007

37. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi

Author: Ropars, Jeanne, Rodriguez De La Vega, Ricardo, Lopez-Villavicencio, Manuela, Gouzy, Jerome, Sallet, Erika, Dumas, Emilie, Lacoste, Sandrine, Debuchy, Robert, Dupont, Joelle, Branca, Antoine, Giraud, Tatiana, Centre National de la Recherche Scientifique (CNRS), Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11), Université Paris-Saclay, Univ. Paris-Sud, AgroParisTech, ANR FROMA-GEN grant [ANR-12-PDOC-0030], Paris-Sud University, ERC starting grant GenomeFun [309403], Marie Curie postdoctoral fellowship (FP7 COFUND PRES-SUD) [246556], ANR grant 'Food, European Project: 309403,EC:FP7:ERC,ERC-2012-StG_20111109,GENOMEFUN(2013), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: convergence, Agricultural and Biological Sciences(all), Gene Transfer, Horizontal, Champignons Penicillium, Biochemistry, Genetics and Molecular Biology(all), [SDV]Life Sciences [q-bio], Penicillium, Adaptation, Biological, Fungi, HGT, Domestication, Fromage, parallel adaptation, Phenotype, Bio-Industrie, Cheese, Report, gene expression, Food Microbiology, food spoiler, DNA, Fungal, Wallaby, CheesyTer
Abstract: Summary Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1–5]. Few studies have focused on the domestication of fungi, with notable exceptions [6–11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making—P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13–15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes., Highlights • New HTRs are found in cheese fungi • HTRs are flanked by specific transposable elements • HTRs have spread in cheese-associated fungi through recent selective sweeps • Experiments link two HTRs to growth and competitive advantages on cheese, Ropars et al. report newly discovered horizontally transferred regions, flanked by specific transposable elements that allow cheese-making fungi and food spoilers to grow faster and be better competitors on cheese. These findings have industrial and food safety implications and also improve our understanding of adaptation processes.
Published: 2015

38. Pea in the genomic era

Author: Burstin , Judith, Alves Carvalho , Susete, Aluome , Christelle, Tayeh , Nadim, Brochot , Anne-Lise, Carrere , Sebastien, Kreplak , Jonathan, Klein , Anthony, Lecomte , Christophe, Bourion , Virginie, Delaitre , Catherine, Falque , Matthieu, Cruaud , Corinne, Salloignon , Pauline, Truntzer , Caroline, Moreau , Sandra, Aubourg-Balzergue , Sandrine, Lejeune-Henaut , Isabelle, Gamas , Pascal, Gouzy , Jerome, Wincker , Patrick, Le Paslier , Marie-Christine, Brunel , Dominique, Aubert , Gregoire, Duc , Gérard, Agroécologie [Dijon], Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique ( INRA ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Plate-forme Protéomique CLIPP - Clinical and Innovation Proteomic Platform [Dijon] ( CLIPP ), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies ( FEMTO-ST ), Université de Technologie de Belfort-Montbeliard ( UTBM ) -Ecole Nationale Supérieure de Mécanique et des Microtechniques ( ENSMM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ) -Université de Technologie de Belfort-Montbeliard ( UTBM ) -Ecole Nationale Supérieure de Mécanique et des Microtechniques ( ENSMM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ) -Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut Charles Viollette (ICV) - EA 7394 ( ICV ), Université d'Artois ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -Université du Littoral Côte d'Opale ( ULCO ) -Institut Supérieur d'Agriculture-Université de Lille, and Etude du Polymorphisme des Génomes Végétaux ( EPGV )
Subjects: [ SDV ] Life Sciences [q-bio], pois, pea
Abstract: BAPPôle Geapsi; Pea in the genomic era. Séminaire IFR AIB (Agrobiosciences, Interactions & Biodiversité)
Published: 2015

39. Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae

Author: Badouin, Hélène, Hood, Michael E., Gouzy, Jérôme, Aguileta, Gabriela, Siguenza, Sophie, Perlin, Michael H., Cuomo, Christina A., Fairhead, Cécile, Branca, Antoine, Giraud, Tatiana, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Amherst College, Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Biology - Program on Disease Evolution, University of Louisville, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Univ. Paris-Sud, European Research Council [309403, ANR-12-ADAP-0009], Institut Diversite et Evolution du Vivant grant, National Science Foundation (NSF) [DEB-1115765, 0947963], Giraud, Tatiana, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Gene Rearrangement, Recombination, Genetic, Basidiomycota, [SDV]Life Sciences [q-bio], Centromere, Microbotryum violaceum, Genomics, Investigations, Telomere, Genes, Mating Type, Fungal, Evolution, Molecular, [SDV] Life Sciences [q-bio], MAT, intratetrad mating, finished genome assembly, selfing, bipolarity, Chromosomes, Fungal, Population and Evolutionary Genetics, basidiomycete
Abstract: International audience; Sex chromosomes in plants and animals and fungal mating-type chromosomes often show exceptional genome features, with extensive suppression of homologous recombination and cytological differentiation between members of the diploid chromosome pair. Despite strong interest in the genetics of these chromosomes, their large regions of suppressed recombination often are enriched in transposable elements and therefore can be challenging to assemble. Here we show that the latest improvements of the PacBio sequencing yield assembly of the whole genome of the anther-smut fungus, Microbotryum lychnidis-dioicae (the pathogenic fungus causing anther-smut disease of Silene latifolia), into finished chromosomes or chromosome arms, even for the repeat-rich mating-type chromosomes and centromeres. Suppressed recombination of the mating-type chromosomes is revealed to span nearly 90% of their lengths, with extreme levels of rearrangements, transposable element accumulation, and differentiation between the two mating types. We observed no correlation between allelic divergence and physical position in the nonrecombining regions of the mating-type chromosomes. This may result from gene conversion or from rearrangements of ancient evolutionary strata, i.e., successive steps of suppressed recombination. Centromeres were found to be composed mainly of copia-like transposable elements and to possess specific minisatellite repeats identical between the different chromosomes. We also identified subtelomeric motifs. In addition, extensive signs of degeneration were detected in the nonrecombining regions in the form of transposable element accumulation and of hundreds of gene losses on each mating-type chromosome. Furthermore, our study highlights the potential of the latest breakthrough PacBio chemistry to resolve complex genome architectures.
Published: 2015

40. Multiple cropping systems as drivers for providing multiple ecosystem services: from concepts to design

Author: Marion Prudent, Elise Pelzer, Sabrina Gaba, Simon Boudsocq, Marie-Laure Navas, Françoise Lescourret, Eric Malézieux, Jérôme Enjalbert, Gaëtan Louarn, Jacques Wery, Harry Ozier-Lafontaine, Etienne-Pascal Journet, Philippe Hinsinger, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Agrosystèmes Cultivés et Herbagers (ARCHE), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (Cirad-Persyst-UPR 103 HORTSYS), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Agronomie, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Agrosystèmes tropicaux (ASTRO), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de recherche Plantes et Systèmes de Culture Horticoles ( PSH ), Institut National de la Recherche Agronomique ( INRA ), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes ( Eco&Sols ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut National de la Recherche Agronomique ( INRA ) -Institut de Recherche pour le Développement ( IRD ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Agrosystèmes Cultivés et Herbagers ( ARCHE ), Institut National Polytechnique [Toulouse] ( INP ) -Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Supérieure Agronomique de Toulouse, Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), UMR LIPM, Centre National de la Recherche Scientifique ( CNRS ), Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Université Paul-Valéry - Montpellier 3 ( UM3 ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -École pratique des hautes études ( EPHE ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens ( SYSTEM ), Institut National de la Recherche Agronomique ( INRA ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères ( P3F ), UR HortSys, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Agrosystèmes tropicaux ( ASTRO ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, F08 - Systèmes et modes de culture, Biodiversité et Ecologie, Multiple cropping, 01 natural sciences, service écosystémique, Interaction biotique, Ecosystem services, Interactions biologiques, Agriculture durable, système de culture, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, 2. Zero hunger, Environmental resource management, 04 agricultural and veterinary sciences, Plant associations, Agroécologie, Agricultural sciences, Agroécosystème, Diversification, P01 - Conservation de la nature et ressources foncières, Culture associée, Biodiversité, Environmental Engineering, Cropping systems, Biotic interactions, Biodiversity and Ecology, Agroecology, Conservation des ressources, Production (economics), Intensification, Sustainable development, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, business.industry, A01 - Agriculture - Considérations générales, Provisioning, Analyse économique, 15. Life on land, services écosystémiques, 13. Climate action, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Plante de culture, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Agronomy and Crop Science, Cropping, Sciences agricoles, 010606 plant biology & botany
Abstract: Provisioning services, such as the production of food, feed, and fiber, have always been the main focus of agriculture. Since the 1950s, intensive cropping systems based on the cultivation of a single crop or a single cultivar, in simplified rotations or monocultures, and relying on extensive use of agrochemical inputs have been preferred to more diverse, self-sustaining cropping systems, regardless of the environmental consequences. However, there is increasing evidence that such intensive agroecosystems have led to a decline in biodiversity as well as threatening the environment and have damaged a number of ecosystem services such as the biogeochemical nutrient cycles and the regulation of climate and water quality. Consequently, the current challenge facing agriculture is to ensure the future of food production while reducing the use of inputs and limiting environmental impacts and the loss of biodiversity. Here, we review examples of multiple cropping systems that aim to use biotic interactions to reduce chemical inputs and provide more ecosystem services than just provisioning. Our main findings are the identification of underlying ecological processes and management strategies related to the provision of pairs of ecosystem services namely food production and a regulation service. We also found gaps between ecological knowledge and the constraints of agricultural practices in taking account of the interactions and possible trade-offs between multiple ecosystem services as well as socioeconomic constraints. We present guidelines for the design of multiple cropping systems combining ecological, agricultural, and genetic concepts and approaches.
Published: 2015

41. Overexpression of BetS, a Sinorhizobium meliloti High-Affinity Betaine Transporter, in Bacteroids from Medicago sativa Nodules Sustains Nitrogen Fixation During Early Salt Stress Adaptation

Author: Alexandre Boscari, Karine Mandon, Daniel Le Rudulier, Ghislaine Van de Sype, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: GABA Plasma Membrane Transport Proteins, Rhizobiaceae, Proline, SINORHIZOBIUM MELILOTI, Osmotic shock, Physiology, Glycine betaine transport, OSMOLARITY, NITROGEN FIXATION, Sodium Chloride, BACTEROID, Betaine transporter, 03 medical and health sciences, chemistry.chemical_compound, NODULES, Betaine, Bacterial Proteins, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Symbiosis, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Sinorhizobium meliloti, Osmotic concentration, biology, 030306 microbiology, food and beverages, hemic and immune systems, General Medicine, biology.organism_classification, Adaptation, Physiological, SALT STRESS, Phenotype, Biochemistry, chemistry, Mutation, Glycine, BETAINE TRANSPORTER, Carrier Proteins, Agronomy and Crop Science, Medicago sativa
Abstract: Sinorhizobium meliloti possesses several betaine transporters to cope with salt stress, and BetS represents a crucial high-affinity glycine and proline betaine uptake system involved in the rapid acquisition of betaines by cells subjected to osmotic upshock. Using a transcriptional lacZ (β-galactosidase) fusion, we showed that betS is expressed during the establishment of the symbiosis and in mature nitrogen-fixing nodules. However, neither Nod nor Fix phenotypes were impaired in a betS mutant. BetS is functional in isolated bacteroids, and its activity is strongly activated by high osmolarity. In bacteroids from a betS mutant, glycine betaine and proline betaine uptake was reduced by 85 to 65%, indicating that BetS is a major component of the overall betaine uptake activity in bacteroids in response to osmotic stress. Upon betS overexpression (strain UNA349) in free-living cells, glycine betaine transport was 2.3-fold higher than in the wild-type strain. Interestingly, the accumulation of proline betaine, the endogenous betaine synthesized by alfalfa plants, was 41% higher in UNA349 bacteroids from alfalfa plants subjected to 1 week of salinization (0.3 M NaCl) than in wild-type bacteroids. In parallel, a much better maintenance of nitrogen fixation activity was observed in 7-day-salinized plants nodulated with the over-expressing strain than in wild-type nodulated plants. Taken altogether, these results are consistent with the major role of BetS as an emergency system involved in the rapid uptake of betaines in isolated and in planta osmotically stressed bacteroids of S. meliloti.
Published: 2006

42. Gene identification in the oomycete pathogen Phytophthora parasitica during in vitro vegetative growth through expressed sequence tags

Author: Eric Galiana, Jo-Yanne Le Berre, Franck Panabières, Joelle Amselem, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Génomique Info (URGI), and Institut National de la Recherche Agronomique (INRA)
Subjects: Phytophthora, 0106 biological sciences, Proteome, Transcription, Genetic, GENE IDENTIFICATION, Genes, Fungal, Molecular Sequence Data, Sequence alignment, OOMYCETE, 01 natural sciences, Microbiology, Fungal Proteins, 03 medical and health sciences, Genetics, FUNCTIONAL CATEGORIZATION, Amino Acid Sequence, Gene, ComputingMilieux_MISCELLANEOUS, Phylogeny, Gene Library, 030304 developmental biology, Expressed Sequence Tags, Oomycete, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Expressed sequence tag, Fungal protein, Base Sequence, Mycelium, biology, cDNA library, fungi, food and beverages, Elicitin, Sequence Analysis, DNA, biology.organism_classification, VIRULENCE, ELICITIN, Sequence Alignment, 010606 plant biology & botany
Abstract: Phytophthora parasitica is a soilborne oomycete pathogen capable of infecting a wide range of plants, including many solanaceous plants. In a first step towards large-scale gene discovery, we generated expressed sequence tags (ESTs) from a cDNA library constructed using mycelium grown in synthetic medium. A total of 3568 ESTs were assembled into 2269 contiguous sequences. Functional categorization could be performed for 65.45% of ESTs. A significant portion of the transcripts encodes proteins of common metabolic pathways. The most prominent sequences correspond to members of the elicitin family, and enzymes involved in the lipid metabolism. A number of genes potentially involved in pathogenesis were also identified, which may constitute virulence determinants.
Published: 2005

43. Construction of Cryptogein Mutants, a Proteinaceous Elicitor from Phytophthora, with Altered Abilities To Induce a Defense Reaction in Tobacco Cells

Author: Tomas Kasparovsky, Antoine Marais, Michel Ponchet, Radka Chaloupková, ⊥ and Jean-Pierre Blein, Hanan Osman, Jiri Damborsky, Vladimír Mikeš, Jan Lochman, Masaryk University [Brno] (MUNI), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Phytopharmacie et Biochimie des Iteractions Cellulaires (PBIC), and Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)
Subjects: 0106 biological sciences, Necrosis, Mutant, Quantitative Structure-Activity Relationship, PHYTOPHTHORA, Ph changes, 01 natural sciences, Biochemistry, Fungal Proteins, CRYPTOGEIN MUTANT, 03 medical and health sciences, Ergosterol, Tobacco, TOBACCO CELL, medicine, Computer Simulation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, SIGNAL PATHWAY, ComputingMilieux_MISCELLANEOUS, Phenylalanine Ammonia-Lyase, Plant Diseases, Plant Proteins, 030304 developmental biology, 0303 health sciences, biology, Circular Dichroism, NECROSIS, Phytophthora cryptogea, Algal Proteins, Fatty Acids, NADPH Oxidases, Proteins, Mycotoxins, Lipid Metabolism, biology.organism_classification, STEROL BINDING, Recombinant Proteins, Elicitor, Active oxygen, Mutagenesis, Site-Directed, ELICITIN, Sterol binding, Phytophthora, medicine.symptom, Reactive Oxygen Species, Protein Binding, 010606 plant biology & botany
Abstract: We prepared a series of cryptogein mutants, an elicitor from Phytophthora cryptogea, with altered abilities to bind sterols and fatty acids. The induction of the early events, i.e., synthesis of active oxygen species and pH changes, in suspension tobacco cells by these mutated proteins was proportional to their ability to bind sterols but not fatty acids. Although the cryptogein-sterol complex was suggested to be a form triggering a defense reaction in tobacco, some proteins unable to bind sterols induced the synthesis of active oxygen species and pH changes. The modeling experiments showed that conformational changes after the introduction of bulky residues into the omega loop of cryptogein resemble those induced by sterol binding. These changes may be necessary for the ability to trigger the early events by elicitins. However, the ability to stimulate necrosis in suspension tobacco cells and the expression of defense proteins in tobacco plants were linked neither to the lipid binding capacity nor to the capacity to provoke the early events. On the basis of these experiments and previous results, we propose that elicitins could stimulate two signal pathways. The first one induces necroses and the expression of pathogen-related proteins, includes tyrosine protein kinases and mitogen-activated protein kinases, and depends on the overall structure and charge distribution. The second type of interaction is mediated by phospholipase C and protein kinase C. It triggers the synthesis of active oxygen species and pH changes. This interaction depends on the ability of elicitins to bind sterols.
Published: 2005

44. Probing the Hydrophobic Cavity of Lipid Transfer Protein from Nicotiana tabacum through Xenon-Based NMR Spectroscopy

Author: Patrick Berthault, Lionel Dubois, Céline Landon, Françoise Vovelle, J. Gaspard Huber, Hervé Desvaux, Pedro Da Silva, Michel Ponchet, Département de Recherche sur l'Etat Condensé, les Atomes et les Molécules (DRECAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 'Interactions Plantes-Microorganismes et Santé Végétale' (U.M.R. - I.P.M.S.V.), Institut National de la Recherche Agronomique (INRA), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Models, Molecular, inorganic chemicals, Xenon, [SDV]Life Sciences [q-bio], Analytical chemistry, chemistry.chemical_element, 010402 general chemistry, 01 natural sciences, Biochemistry, Catalysis, Colloid and Surface Chemistry, Chemical affinity, Tobacco, Isotopes of xenon, Molecule, Computer Simulation, cardiovascular diseases, Nuclear Magnetic Resonance, Biomolecular, Plant Proteins, integumentary system, 010405 organic chemistry, Chemical shift, Noble gas, General Chemistry, Nuclear magnetic resonance spectroscopy, Antigens, Plant, Binding constant, 0104 chemical sciences, Solutions, Kinetics, Crystallography, chemistry, Thermodynamics, Carrier Proteins, Hydrophobic and Hydrophilic Interactions, circulatory and respiratory physiology
Abstract: The hydrophobic cavity of Lipid Transfer Protein 1 from Nicotiana tabacum is investigated in detail by NMR using xenon as a spy. The analysis of the (129)Xe chemical shifts and self-relaxation times gives evidence of protein-xenon interaction. Thermodynamics of the binding is characterized through the study of aliphatic (1)H and (13)C chemical shift variation as a function of xenon pressure. The binding constant is evaluated to 75.5 +/- 1.0 M(-1) at 293 K. The location of xenon inside the cavity is deduced from SPINOE experiments. The noble gas appears to occupy four sites, and xenon self-relaxation experiments indicate that it quickly jumps between different sites. The chemical shifts of amide protons and nitrogens also depend on the xenon concentration, either specifically or nonspecifically for atoms at the external surface of the protein. Yet, contrary to aliphatic atoms, they do not correspond to short-range interactions as confirmed by magnetization transfer experiments between laser-polarized xenon and protons in H(2)O. These (15)N chemical shift variations, used in combination with (15)N transverse self-relaxation rates to determine the lower limit of the binding rate, consequently reveal subtle changes in the structure of the protein upon binding.
Published: 2004

45. Modulation of the Biological Activity of a Tobacco LTP1 by Lipid Complexation

Author: Nathalie Buhot, José Lequeu, Eric Gomès, Didier Marion, Jean-Pierre Blein, Serge Delrot, ML Milat, Pierre Coutos-Thévenot, Michel Ponchet, Transport des assimilats (TA), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale (IPMSV), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA), Unité de recherche biopolymeres interactions assemblages (BIA), Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Phytopharmacie et Biochimie des Iteractions Cellulaires (PBIC), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), UR 0724 Unité de recherche Biochimie et technologie des protéines, and Institut National de la Recherche Agronomique (INRA)-Transformation des Produits Végétaux (T.P.V.)-Unité de recherche Biochimie et technologie des protéines (NANT LBTP)
Subjects: Phytophthora, 0106 biological sciences, [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, Cyclopentanes, Plasma protein binding, Biology, Fatty Acid-Binding Proteins, Ligands, 01 natural sciences, Mass Spectrometry, Fatty acid-binding protein, Cell membrane, 03 medical and health sciences, chemistry.chemical_compound, Tobacco, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Extracellular, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Oxylipins, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Dose-Response Relationship, Drug, Circular Dichroism, Jasmonic acid, Cell Membrane, Fatty Acids, Elicitin, Biological activity, Articles, Cell Biology, [SDV.IDA] Life Sciences [q-bio]/Food engineering, Lipid Metabolism, Lipids, Recombinant Proteins, medicine.anatomical_structure, Biochemistry, chemistry, PHYTOPHTORA PARASITICA, Carrier Proteins, TRANSFERT LIPIDIQUE, Plant lipid transfer proteins, Chromatography, Liquid, Protein Binding, 010606 plant biology & botany
Abstract: Plant lipid transfer proteins (LTPs) are small, cysteine-rich proteins secreted into the extracellular space. They belong to the pathogenesis-related proteins (PR-14) family and are believed to be involved in several physiological processes including plant disease resistance, although their precise biological function is still unknown. Here, we show that a recombinant tobacco LTP1 is able to load fatty acids and jasmonic acid. This LTP1 binds to specific plasma membrane sites, previously characterized as elicitin receptors, and is shown to be involved in the activation of plant defense. The biological properties of this LTP1 were compared with those of LTP1-linolenic and LTP1-jasmonic acid complexes. The binding curve of the LTP1-linolenic acid complex to purified tobacco plasma membranes is comparable to the curve obtained with LTP1. In contrast, the LTP1-jasmonic acid complex shows a strongly increased interaction with the plasma membrane receptors. Treatment of tobacco plants with LTP1-jasmonic acid resulted in an enhancement of resistance toward Phytophthora parasitica. These effects were absent upon treatment with LTP1 or jasmonic acid alone. This work presents the first evidence for a biological activity of a LTP1 and points out the crucial role of protein-specific lipophilic ligand interaction in the modulation of the protein activity.
Published: 2004

46. Marker-assisted selection for the wide-spectrum resistance to root-knot nematodes conferred by the Ma gene from Myrobalan plum (Prunus cerasifera) in interspecific Prunus material

Author: Anne-Claire Lecouls, Jean-Luc Poëssel, G. Salesses, Daniel Esmenjaud, A. Bonnet, Maria-Jose Rubio-Cabetas, Roger Voisin, Mireille Faurobert, Véronique Bergougnoux, N. Bosselut, Elisabeth Dirlewanger, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), and Unité de recherches Espèces Fruitières et Vigne (UREFV)
Subjects: 0106 biological sciences, PRUNUS AMYGDALUS, Plant Science, 01 natural sciences, Prunus cerasifera, 03 medical and health sciences, Prunus, PRUNIER, Botany, Genetics, Root-knot nematode, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Hybrid, 0303 health sciences, Genetic diversity, biology, AMANDIER, food and beverages, Marker-assisted selection, biology.organism_classification, Rootstock, Agronomy and Crop Science, Terra incognita, 010606 plant biology & botany, Biotechnology
Abstract: Prunus species express a more or less wide spectrum of resistance to root-knot nematodes (RKN) of the genus Meloidogyne. Among them, sources from Myrobalan plum (P. cerasifera) control all major and minor RKN species tested. In this outbreeding species, the clones P.2175 and P.2980 are heterozygous for the Ma single dominant gene and carry the alleles Ma1 and Ma3, respectively. Each allele confers a high-level resistance to the predominant RKN, M. arenaria, M. incognita and M. javanica and to the Florida isolate of an unknown Meloidogyne sp. which overcomes the resistance from peach and almond sources. The polymorphism of two coupling-phase SCAR markers tightly linked to Ma, SCAL19690 and SCAFLP2202, was evaluated within diverse diploid Prunus accessions. This material belongs to the subgenera Prunophora (Myrobalan and apricot) or Amygdalus (peach, almond and almond-peach) and includes the RKN resistance sources ‘Nemared’, ‘Alnem 1’ and ‘GF.557’. The alleles SCAL19690 and SCAFLP2202 were not present in three apricot cultivars (‘Moniqui’, ‘Luizet’ and ‘Stark Early Orange’) representative of the genetic diversity of this species and they segregated in an interspecific cross between P.2980 and apricot. These results suggest that apricot, reported as resistant to M. arenaria, M. incognita and M. javanica, and the Myrobalan plum might possess two different resistance systems. SCAL19690 and SCAFLP2202 were also absent from all tested Amygdalus material, whatever its resistance to RKN. Eight Myrobalan×Amygdalus segregating progenies including bispecific (P.2175 or P.2980×peach or almond) and trispecific (P.2175 or P.2980×almond-peach) hybrids were tested with the Florida isolate to identify individuals carrying the Ma resistance alleles. Both SCARs were then evaluated for segregation in these progenies to develop marker-assisted selection of Prunus interspecific rootstocks. SCAL19690 and SCAFLP2202 could be clearly detected and their tight linkage to Ma1 and Ma3 was confirmed. Consequently these SCARs appear to be powerful tools to screen for RKN resistance conferred by the Ma gene. They should also facilitate marker-assisted pyramiding of Ma with other resistance genes from the Amygdalus subgenus or from the botanically-related Armeniaca section.
Published: 2004

47. Spectrum and inheritance of resistance to the root-knot nematode Meloidogyne hapla in Rosa multiflora and R. indica

Author: J. Bazzano, S. Mastrantuono, Y. Jacob, X. Wang, Roger Voisin, Daniel Esmenjaud, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Unité d'amélioration des plantes florales de Fréjus (ANTIB FREJUS UE), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Rosa multiflora, Rosaceae, Plant Science, medicine.disease_cause, 01 natural sciences, Diallel cross, 03 medical and health sciences, RESISTANCE AUX ORGANISMES NUISIBLES, Botany, Infestation, Genetics, medicine, biology.hybrid_parent_classification, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Root-knot nematode, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, biology.organism_classification, Horticulture, Nematode, Rootstock, Agronomy and Crop Science, Terra incognita, 010606 plant biology & botany
Abstract: The spectrum and inheritance of resistance to the root-knot nematode Meloidogyne hapla was studied in the diploid species Rosa multiflora and R. indica. The host suitability of seven rose rootstocks, namely five R. multiflora (K2, K1, Floradale, CE63 and CE65) and two R. indica (CE35 and Maroc) clonal accessions, was evaluated using four geographic isolates of M. hapla. Plants grown under greenhouse conditions were tested at high and durable inoculum pressure of nematodes and rated for nematode infestation five months after inoculation on a 0–5 gall index. Different host suitabilities to M. hapla were demonstrated depending on the nematode isolates: in R. multiflora, the clone K2 had a resistant (R) response to all isolates; the clone K1 ranged from intermediate (I) (isolate ‘Canada’) to resistant (other isolates), Floradale was shown to be intermediate, whereas CE63 and CE65 were moderate to good hosts (H). In R. indica, both rootstocks were good to excellent hosts for the isolate Canada but resistant to all three other isolates, thus expressing an isolate-specific resistance. A study on the genetics of resistance in R. multiflora to the M. hapla isolate Canada was then conducted using an incomplete diallel cross involving all previous clones except Floradale. A total of 120 hybrid individuals belonging to several progenies representing the cross combinations R × I, R × H, I × H and H × H were evaluated. Individuals of each progeny generally ranged into a monomodal distribution that suggests polygenic inheritance of resistance. In the family Rosaceae, the differences in the resistance genetics to the meiotic species M. hapla and to the mitotic species, M. arenaria, M. incognita and M. javanica are discussed in relation to the reproductive status of the nematodes.
Published: 2004

48. A Set of Genes Differentially Expressed Between Avirulent and Virulent Meloidogyne incognita Near-Isogenic Lines Encode Secreted Proteins

Author: Pierre Abad, Philippe Castagnone-Sereno, Stéphanie Jaubert, Cédric Neveu, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Signal peptide, DNA, Complementary, Physiology, Virulence, Biology, 01 natural sciences, 03 medical and health sciences, Complementary DNA, Gene expression, Meloidogyne incognita, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Tylenchoidea, Cloning, Molecular, Gene, In Situ Hybridization, ComputingMilieux_MISCELLANEOUS, DNA Primers, 030304 developmental biology, Genetics, 0303 health sciences, Base Sequence, Reverse Transcriptase Polymerase Chain Reaction, food and beverages, Helminth Proteins, General Medicine, biology.organism_classification, POUVOIR PATHOGENE, Gene Expression Regulation, Amplified fragment length polymorphism, Agronomy and Crop Science, Terra incognita, Subcellular Fractions, 010606 plant biology & botany
Abstract: A cDNA-amplification fragment length polymorphism (AFLP)-based strategy has been used to identify genes differentially expressed between two pairs of near-isogenic lines (NIL) of the root-knot nematode Meloidogyne incognita either avirulent or virulent against the tomato Mi resistance gene. Gene expression profiles from infective second-stage juveniles (J2) were compared, and 22 of the 24,025 transcript-derived fragments (TDF) generated proved to be differential, i.e., present in both avirulent NIL and absent in both virulent NIL. Fourteen of the TDF sequences did not show any significant similarity to known proteins, while eight matched reported sequences from nematodes and other invertebrates. The differential expression of nine genes was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) experiments. In situ hybridization conducted with five of the sequences showed that two were specifically expressed in the intestinal cells (HM10 and PM1), one in the subventral esophageal glands (HM1), and two in the dorsal esophageal gland of J2 (HM7 and HM12). Analysis of full-length cDNA sequences revealed the presence of a signal peptide for HM1, HM10, and HM12, indicating that the encoded proteins are putatively secreted. Since secreted products in general and esophageal gland secretions in particular are thought to be among the main M. incognita pathogenicity factors, this result suggests a possible dual role for some of the genes encoding such secretions, i.e., they could be involved in both pathogenicity and virulence or avirulence of these biotrophic parasites.
Published: 2003

49. RESISTANCE TO BIOTIC STRESS IN FRUIT TREES

Author: Jean-Luc Poëssel, Albertus Eskes, Daniel Esmenjaud, Yves Lespinasse, Charles Eric Durel, Unité mixte de recherche génétique et horticulture Genhort, Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Génétique et Amélioration des Fruits et Légumes (GAFL), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Résistance génétique, [SDV]Life Sciences [q-bio], Sélection, Coffea, Podosphaera leucotricha, Asexual reproduction, 01 natural sciences, F30 - Génétique et amélioration des plantes, Gene flow, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, food and beverages, Hemileia vastatrix, AMELIORATION DES PLANTES, Major gene, Malus, Fire blight, Prunus, Venturia inaequalis, Meloidogyne, Population, Horticulture, Quantitative trait locus, Biology, Arbre, 03 medical and health sciences, Résistance aux facteurs nuisibles, Erwinia amylovora, Mycosphaerella fijiensis, education, Durabilité, H20 - Maladies des plantes, 030304 developmental biology, business.industry, Musa, Biotic stress, biology.organism_classification, H10 - Ravageurs des plantes, Biotechnology, business, Fruit tree, 010606 plant biology & botany
Abstract: Resistance to pests and diseases is a highly desirable objective in fruit breeding but is a long-term endeavor. It requires appropriate tests for early screening and an analysis of host-parasite interactions for durability of resistance. Host resistance is considered durable when it remains effective for a long period despite an intensive exposure to the parasite. Durability has to be the key-point of any fruit breeding programme for resistance. Non-durable resistance is usually associated with a hypersensitive reaction (HR) and major gene resistance which often occur in multiple allelic series and/or complex loci. HR resistance or race-specific resistance is often rendered ineffective because the pathogen population shifts genetically to avoid the resistance gene. Resistance of a more durable nature against fungi and bacteria is often polygenic and based upon the additive or interaction effects of a few to several genes not promoting a hypersensitive reaction. The more complex the genetics of the resistance, the more difficult it is for the pathogen to evolve to a form that can overcome the resistance. Polygenic resistance is usually associated with a quantitative expression that is characterized by a continuous variation between susceptibility and resistance. To approach the number of genes involved in polygenic resistance (QTL) and the relative effect of each of these genes, they have to be mapped on the genome. Marker-assisted selection (MAS) gives the possibility to recombine QTL for resistance; major genes could be associated with QTL. The combining of resistance genes is desired to: acquire a higher level of resistance against a particular pathotype, obtain resistance against a broader range of pathotypes, and combine different mechanisms of resistance. The current situation of fruit crops - monocultivar orchards established for several years - enhances the selection pressure on the pathogen population and results in population shifts which could be dramatic. Guidelines have to be proposed to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure; the most important parameters to consider are reproductive/mating systems and gene/genotype flow. Pathogens that have the greatest risk of breaking down resistance genes are those that possess a mixed reproduction system, with one sexual cycle per growing season and asexual reproduction during the epidemic phase, and a high potential for gene flow. Several examples of different strategies used by fruit breeders will be reported mainly on Coffea (coffee rust), Musa (black leaf streak disease), Prunus (root knot nematodes) and Malus (scab, mildew, fire blight). Fruit breeders can use the lessons learned from deploying resistance genes in annual crops and selecting resistance in forest trees and apply these to their strategies for fruit tree improvement
Published: 2003

50. A Tobacco S-like RNase Inhibits Hyphal Elongation of Plant Pathogens

Author: Antoine Marais, Pierre Ricci, Karine Hugot, Michel Ponchet, Eric Galiana, Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Hyphal growth, Physiology, RNase P, Phenylalanine, Nicotiana tabacum, RELATION HOTE PATHOGENE, Polymerase Chain Reaction, 01 natural sciences, Pichia, 03 medical and health sciences, Ribonucleases, Fusarium, Tobacco, Botany, Gene expression, Extracellular, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Histidine, Ribonuclease, ComputingMilieux_MISCELLANEOUS, DNA Primers, Plant Diseases, Plant Proteins, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Base Sequence, biology, fungi, food and beverages, RNA, General Medicine, biology.organism_classification, Cell biology, Amino Acid Substitution, Oomycetes, REPONSE DE LA PLANTE, Mutagenesis, Site-Directed, biology.protein, Agronomy and Crop Science, Pollen-pistil interaction, 010606 plant biology & botany
Abstract: Ribonuclease (RNase) NE gene expression is induced in tobacco leaves in response to Phytophthora parasitica. Using antibodies directed against RNase NE, we demonstrate that RNase NE is extracellular at the early steps of the interaction, while the fungal tip growth is initiated in the apoplas-tic compartment. After production in Pichia pastoris and biochemical purification, we show that the S-like RNase NE inhibits hyphal growth from P. parasitica zoospores and from Fusarium oxysporum conidia in vitro. Conversion into an enzymatically inactive form after mutagenesis of the active site-histidine 97 residue to phenylalanine leads to the suppression of this activity, suggesting that RNase NE inhibits the elongation of germ tubes by degradation of microbial RNAs. Exogenous application of RNase NE in the extracellular space of leaves inhibits the development of P. parasitica. Based on its induction by inoculation, its localization, and its activity against two plant pathogens, we propose that RNase NE participates in tobacco defense mechanisms by a direct action on hyphal development in the extracellular space. The RNase activity-dependent antimicrobial activity of the S-like RNase NE shares similarities with the only other biological activity demonstrated for plant RNases, the inhibition of elongation of pollen tubes by the S-RNase in gametophytic self-incompatibility, suggesting a functional link between self and nonself interactions in plants.
Published: 2002

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