Author: "François Artiguenave" / Topic: 0303 health sciences - Searchworks@Jio Institute Digital Library Search Results

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22 results on '"François Artiguenave"'

1. 3-Keto-5-aminohexanoate Cleavage Enzyme

Author: Marco Bellinzoni, François Artiguenave, Pedro M. Alzari, Anne Zaparucha, Carine Vergne, Georges N. Cohen, Raquel C. de Melo-Minardi, Nadia Perchat, Alain Perret, Karine Bastard, Jean Weissenbach, Marcel Salanoubat, and Tristan Wagner
Subjects: chemistry.chemical_classification, 0303 health sciences, Claisen condensation, Chemistry, Stereochemistry, Oxo-Acid-Lyases, Cell Biology, 010402 general chemistry, Lyase, 01 natural sciences, Biochemistry, Enzyme structure, 0104 chemical sciences, Triosephosphate isomerase, 03 medical and health sciences, Protein structure, Enzyme, TIM barrel, Molecular Biology, 030304 developmental biology
Abstract: The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long known as being involved in the anaerobic fermentation of lysine but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn2+ cation reminiscent of metal-dependent class II aldolases, our results based on a combination of x-ray snapshots and molecular modeling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the “domain of unknown function” DUF849.
Published: 2011
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2. 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
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3. In Vitro and In Vivo Modulation of Alternative Splicing by the Biguanide Metformin

Author: Anne Boland, Jean-François Deleuze, Sandrine Baghdoyan, Cécile Martinat, Sylvia Franc, Emilie Chautard, Marc Peschanski, Christophe Battail, Xavier Nissan, François Artiguenave, Laetitia Barrault, Jacqueline Gide, Pierre Rustin, Guillaume Charpentier, Clara Benoit, Didier Auboeuf, Paule Bénit, Guillaume Bassez, Delphine Laustriat, Denis Furling, Centre d'Etude des Cellules Souches (CECS), AFM, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard [Lyon] - Université Claude Bernard Lyon 1 (UCBL) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive (LBBE), Université Claude Bernard Lyon 1 (UCBL) - Institut National de Recherche en Informatique et en Automatique (Inria) - Centre National de la Recherche Scientifique (CNRS), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Neuroprotection du Cerveau en Développement (PROTECT), Assistance publique - Hôpitaux de Paris (AP-HP) - Hôpital Robert Debré - Université Paris Diderot - Paris 7 (UP7) - Institut National de la Santé et de la Recherche Médicale (INSERM), Faculté de Médecine, Université Paris Diderot - Paris 7 (UP7), Centre d'études et de recherches pour l'intensification du traitement du diabète (CERITD), Centre Hospitalier Sud Francilien, CH Evry-Corbeil, Centre de recherche en myologie, Université Pierre et Marie Curie - Paris 6 (UPMC) - AFM - Institut National de la Santé et de la Recherche Médicale (INSERM) - Centre National de la Recherche Scientifique (CNRS), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM) - Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12) - IFR10, Institut des cellules souches pour le traitement et l'étude des maladies monogéniques (I-STEM), Université d'Evry-Val d'Essonne - Institut National de la Santé et de la Recherche Médicale (INSERM), Association française contre les myopathies (AFM-Téléthon), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Baobab, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Neuroprotection du Cerveau en Développement / Promoting Research Oriented Towards Early Cns Therapies (PROTECT), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot - Paris 7 (UPD7), Université Pierre et Marie Curie - Paris 6 (UPMC)-Association française contre les myopathies (AFM-Téléthon)-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)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Généthon, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10
Subjects: AMPK, medicine.drug_class, RBM3, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, Myotonic dystrophy, 03 medical and health sciences, alternative splicing, 0302 clinical medicine, Downregulation and upregulation, Drug Discovery, medicine, myotonic dystrophy type 1, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Biguanide, lcsh:RM1-950, Alternative splicing, medicine.disease, Metformin, 3. Good health, lcsh:Therapeutics. Pharmacology, Mechanism of action, RNA splicing, Cancer research, Molecular Medicine, Original Article, medicine.symptom, 030217 neurology & neurosurgery, medicine.drug
Abstract: International audience; Major physiological changes are governed by alternative splicing of RNA, and its misregulation may lead to specific diseases. With the use of a genome-wide approach, we show here that this splicing step can be modified by medication and demonstrate the effects of the biguanide metformin, on alternative splicing. The mechanism of action involves AMPK activation and downregulation of the RBM3 RNA-binding protein. The effects of metformin treatment were tested on myotonic dystrophy type I (DM1), a multisystemic disease considered to be a spliceopathy. We show that this drug promotes a corrective effect on several splicing defects associated with DM1 in derivatives of human embryonic stem cells carrying the causal mutation of DM1 as well as in primary myoblasts derived from patients. The biological effects of metformin were shown to be compatible with typical therapeutic dosages in a clinical investigation involving diabetic patients. The drug appears to act as a modifier of alternative splicing of a subset of genes and may therefore have novel therapeutic potential for many more diseases besides those directly linked to defective alternative splicing.
Published: 2015
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4. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Author: Tristan Barbeyron, Wilfrid Carré, Michael Katinka, Loraine Brillet, Klaus Valentin, Karine Labadie, Betina M. Porcel, Zofia Nehr, Francisco Cabello-Hurtado, Mirjam Czjzek, Benjamin Noel, Philippe Deschamps, Susana M. Coelho, John H. F. Bothwell, Pascal J. Lopez, Marek Eliáš, François Artiguenave, François-Yves Bouget, Thierry Tonon, Jean Weissenbach, Christophe Colleoni, Deirdre H. McLachlan, Ahmed A. Moustafa, Cécile Hervé, Olivier Panaud, Catherine Boyen, Jonas Collén, Antonios Zambounis, Frédéric Partensky, Cristian Chaparro, Ludovic Delage, Jose Fernandes Barbosa-Neto, Salvador Capella-Gutierrez, Bernard Kloareg, Nathalie Kowalczyk, Gaelle Samson, Gurvan Michel, Simon M. Dittami, Jean-Marc Aury, J. Mark Cock, Patrick Wincker, Agnès Groisillier, Pi Nyvall Collén, Bénédicte Charrier, Corinne Da Silva, Catherine Leblanc, Lionel Cladière, Alok Arun, Laurence Meslet-Cladiere, Claire M. M. Gachon, Sylvie Rousvoal, Kamel Jabbari, Stefan A. Rensing, Toni Gabaldón, Steven G. Ball, Aikaterini Symeonidi, Julie Poulain, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Department of Plant Physiology, Faculty of Sciences, Charles University [Prague] (CU), Belfast e-Science Centre [Belfast] (BESC), Queen's University [Belfast] (QUB), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Scottish Association for Marine Science (SAMS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), 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-PSL), 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), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, University of Freiburg [Freiburg], Freiburg Initiative in Systems Biology, Centre for Research and Technology Hellas (CERTH), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Charles University [Prague], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona], Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), 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), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Center for Research and Technology Hellas, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), 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), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Transposable element, Genome evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Bacterial genome size, Biology, Chondrus, MESH: Base Sequence, MESH: RNA, Plant, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, MESH: Genes, Plant, 14. Life underwater, Gene, Genome size, MESH: Evolution, Molecular, 030304 developmental biology, Plant Proteins, Genetics, 0303 health sciences, Multidisciplinary, MESH: Molecular Sequence Data, Base Sequence, MESH: Plant Proteins, Archaeplastida, Biological Sciences, biology.organism_classification, MicroRNAs, RNA, Plant, MESH: MicroRNAs, MESH: Chondrus, 010606 plant biology & botany
Abstract: Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.
Published: 2013
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5. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining

Author: Pierre Abad, Etienne Danchin, Amandine Campan-Fournier, Nicolas Nottet, Marc Magliano, François Artiguenave, Martine Da Rocha, Marie-Jeanne Arguel, Karine Labadie, Laetitia Perfus-Barbeoch, Julie Guy, Corinne Da Silva, Marie-Noëlle Rosso, Danchin, Etienne, Institut Sophia Agrobiotech (ISA), 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), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), 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), ANR NEMATARGETS, 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), 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)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, interférence à arn, parasitisme, 01 natural sciences, Genome, RNA interference, gène cible, Meloidogyne incognita, nématode à galles, lcsh:QH301-705.5, protéome, pathologie végétale, Genes, Helminth, gène régulateur, 2. Zero hunger, Genetics, 0303 health sciences, Vegetal Biology, Effector, Pan-genome, food and beverages, santé humaine, nématicide, Agricultural sciences, lutte contre les ravageurs, ravageur de culture, pollution environnementale, RNA Interference, Research Article, lcsh:Immunologic diseases. Allergy, nématode des plantes, Immunology, phytopathologie, Biology, approche génomique, Microbiology, identification de gènes, nématode parasite, 03 medical and health sciences, interaction plante parasite, Virology, Botany, Animals, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, séquence silencer, Tylenchoidea, Molecular Biology, Gene, Plant Diseases, 030304 developmental biology, Comparative genomics, biology.organism_classification, meloidogyne incognita, Nematode, lcsh:Biology (General), génie génétique, Parasitology, lcsh:RC581-607, Sciences agricoles, Biologie végétale, Genome-Wide Association Study, 010606 plant biology & botany
Abstract: Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means., Author Summary Plant-parasitic nematodes are annually responsible for more than $100 billion crop yield loss worldwide and those considered as causing most of the damages are root-knot nematodes. These nematodes used to be controlled by chemicals that are now banned from use because of their poor specificity and high toxicity for the environment and human health. In the absence of sustainable alternative solutions, new control means, more specifically targeted against these nematodes and safe for the environment are needed. We searched in root-knot nematode genomes, genes conserved in various plant-damaging species while otherwise absent from the genomes of non target species such as those of chordates, plants, annelids, insect pollinators and mollusks. These genes are probably important for plant parasitism and their absence from non-target species make them interesting candidates for the development of more specific and safer control means. Further bioinformatics pruning of this set of genes yielded 16 novel candidates that could be biologically tested. Using RNA interference, we knocked down each of these 16 genes in a root-knot nematode and tested the effect on plant parasitism efficiency. Out of the 16 tested genes, 12 showed a significant and reproducible diminution of infestation when silenced and are thus particularly promising.
Published: 2013
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6. Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

Author: Julie Poulain, Jean-Marc Aury, Marie Diogon, Patrick Wincker, Céline Brochier-Armanet, Arnaud Couloux, Nicolas Blot, Kevin S. W. Tan, Catherine Texier, François Artiguenave, Geok Choo Ng, Véronique Anthouard, Christian P. Vivarès, Béatrice Segurens, Michaël Roussel, Eric Viscogliosi, Frédéric Delbac, Hicham El Alaoui, Corinne Da Silva, Benjamin Noel, Olivier Jaillon, Ivan Wawrzyniak, Philippe Poirier, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Molecular and Cellular Parasitology, National University of Singapore (NUS), 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), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), and BMC, Ed.
Subjects: Candidate gene, Gene Transfer, Horizontal, Proteome, Virulence Factors, [SDV.GEN] Life Sciences [q-bio]/Genetics, Mitochondrion, Genome, Antioxidants, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, Symbiosis, 030304 developmental biology, Whole genome sequencing, Genetics, 0303 health sciences, Blastocystis, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Base Sequence, 030306 microbiology, Effector, Research, biology.organism_classification, Drug Resistance, Multiple, 3. Good health, Mitochondria, Horizontal gene transfer, Host-Pathogen Interactions, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genome, Protozoan, Metabolic Networks and Pathways, Stramenopiles
Abstract: International audience; ABSTRACT: BACKGROUND: Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified different subtypes but no one subtype has been definitively correlated with disease. RESULTS: Here we report the 18.8 Mb genome sequence of a Blastocystis subtype 7 isolate, which is the smallest stramenopile genome sequenced to date. The genome is highly compact and contains intriguing rearrangements. Comparisons with other available stramenopile genomes (plant pathogenic oomycete and diatom genomes) revealed effector proteins potentially involved in the adaptation to the intestinal environment, which were likely acquired via horizontal gene transfer. Moreover, Blastocystis living in anaerobic conditions harbors mitochondria-like organelles. An incomplete oxidative phosphorylation chain, a partial Krebs cycle, amino acid and fatty acid metabolisms and an iron-sulfur cluster assembly are all predicted to occur in these organelles. Predicted secretory proteins possess putative activities that may alter host physiology, such as proteases, protease-inhibitors, immunophilins and glycosyltransferases. This parasite also possesses the enzymatic machinery to tolerate oxidative bursts resulting from its own metabolism or induced by the host immune system. CONCLUSIONS: This study provides insights into the genome architecture of this unusual stramenopile. It also proposes candidate genes with which to study the physiopathology of this parasite and thus may lead to further investigations into Blastocystis-host interactions.
Published: 2011
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7. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Author: Fekadu Yadetie, Eric Westhof, Julie Poulain, Jean-Marc Aury, John H. Postlethwait, Claire Jubin, Scott William Roy, Atsuo Nishino, Matthieu Muffato, Lisbeth C. Olsen, Hiroki Nishida, Anke Konrad, Véronique Anthouard, Jean Weissenbach, Sutada Mungpakdee, Hugues Roest Crollius, Stephen Butcher, Corinne Da Silva, Evelyne Huynh Cong, Louis Du Pasquier, Helen Eikeseth-Otteraa, Jana Mikhaleva, Benjamin Noel, François Artiguenave, Marit Flo Jensen, Olivier Jaillon, David A. Liberles, Simon Henriet, Jean-Nicolas Volff, Henner Brinkmann, Sarabdeep Singh, Alexandra Louis, Pascal Chourrout, Coen Campsteijn, Marcin Adamski, Jean-Marie Bouquet, Cristian Cañestro, J. Robert Manak, Daniel Chourrout, Hervé Philippe, Gemma B. Danks, Hans Lehrach, Eric M. Thompson, Richard Reinhardt, Boris Lenhard, Snehalata Huzurbazar, Rym Kachouri-Lafond, Pierre Boudinot, Ismael Cross, Georgia Tsagkogeorga, Betina M. Porcel, Matteo Ugolini, Rein Aasland, Frédéric Delsuc, Patrick Wincker, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), SARS International Centre for Marine Molecular Biology, 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), Canadian Institute for Advanced Research (CIAR), Université de Montréal [Montréal], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Neuroscience, University of Oregon, Eugene, Oregon, University of Oregon [Eugene], Laboratorio de Genética, Universidad de Cádiz, Cádiz, Universidad de Cádiz (UCA), DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), 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)-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), Department of Biology, University of Iowa, Iowa City, University of Iowa [Iowa City], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Biology, University of Wyoming, Laramie, University of Wyoming (UW), Department of Statistics, University of Wyoming, Laramie, Enseignement-Formation-Apprentissage (EFA), Université de Mons-Hainaut, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-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, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, Osaka University, Osaka, Osaka University [Osaka], American Hospital of Paris, Hôpital Américain de Paris, University of Bergen (UIB), Department of Vertebrate Genomics [Berlin], Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, National Center for Biotechnology Information (NCBI), Institute of Neuroscience, University of Oregon, Eugene, Institute of Zoology and Evolutionary Biology, University of Basel (Unibas), Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Canadian Institute for Advanced Research (CIFAR), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), 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-PSL), 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)-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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), University of Bergen (UiB), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), NSF [IOS-0719577, DBI-0743374], 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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, 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)-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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), 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)-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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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 Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0106 biological sciences, GENES, Lineage (evolution), Molecular Sequence Data, Chordate, 010603 evolutionary biology, 01 natural sciences, Genome, Synteny, Article, INTRON, 03 medical and health sciences, Genes, Duplicate, Gene Order, [SDE.BE.EVO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.evo, Animals, 14. Life underwater, Urochordata, Gene, 030304 developmental biology, Genetics, Recombination, Genetic, 0303 health sciences, Multidisciplinary, COMPLEXITY, biology, Genes, Homeobox, Exons, biology.organism_classification, Biological Evolution, Invertebrates, OIKOPLEURA-DIOICA, Introns, Oikopleura, Sister group, Evolutionary biology, ORIGINS, Vertebrates, DNA Transposable Elements, Spliceosomes, Oikopleura dioica, DNA, Intergenic, CAENORHABDITIS-ELEGANS
Abstract: Ocean Dweller Sequenced The Tunicates, which include the solitary free-swimming larvaceans that are a major pelagic component of our oceans, are a basal lineage of the chordates. In order to investigate the major evolutionary transition represented by these organisms, Denoeud et al. (p. 1381 , published online 18 November) sequenced the genome of Oikopleura dioica , a chordate placed by phylogeny between vertebrates and amphioxus. Surprisingly, the genome showed little conservation in genome architecture when compared to the genomes of other animals. Furthermore, this highly compacted genome contained intron gains and losses, as well as species-specific gene duplications and losses that may be associated with development. Thus, contrary to popular belief, global similarities of genome architecture from sponges to humans are not essential for the preservation of ancestral morphologies.
Published: 2010
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8. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author: Jean-Marc Aury, Frithjof C. Küpper, Diego Miranda-Saavedra, John H. F. Bothwell, Claire Jubin, Chris Bowler, Bernhard Gschloessl, James W. Tregear, Andrés Ritter, Andrew E. Allen, Carolyn A. Napoli, Ludovic Delage, Bernard Kloareg, Takahiro Yamagishi, Pi Nyvall-Collén, Svenja Heesch, Julia Morales, Gaelle Samson, Kei Kimura, Ga Youn Cho, Grigoris D. Amoutzias, Yves Van de Peer, Simon M. Dittami, Kenny Billiau, Julie Poulain, François Artiguenave, Sylvie Doulbeau, Marek Eliáš, Bank Beszteri, Carl J. Carrano, Daniel Lang, Florian Maumus, Stefan A. Rensing, Jonathan H. Badger, Béatrice Segurens, Martina Strittmatter, Sylvie Rousvoal, Hervé Moreau, Patrice Lerouge, Colin Brownlee, Betsy Read, Akira F. Peters, J. Mark Cock, Corinne Da Silva, Declan C. Schroeder, Catherine Boyen, Pierre Rouzé, Eric Bonnet, Jonas Collén, Susana M. Coelho, Aude Le Bail, Kamel Jabbari, David R. Nelson, Thierry Tonon, Pascal J. Lopez, Véronique Anthouard, Hadi Quesneville, Manoj P. Samanta, Delphine Scornet, Klaus Valentin, Nicolas Delaroque, Bénédicte Charrier, Cindy Martens, Peter von Dassow, Martin Lohr, Garry Farnham, Chikako Nagasato, Claire M. M. Gachon, Gurvan Michel, Lieven Sterck, Philippe Potin, Erwan Corre, Catherine Leblanc, Taizo Motomura, Cyril Pommier, Patrick Wincker, Hiroshi Kawai, Publica, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, J Craig Venter Institute, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Marine Biological Association, 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), San Diego State University (SDSU), Phophorylation de protéines et Pathologies Humaines (P3H), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Charles University [Prague], Scottish Association for Marine Science (SAMS), Kobe University, Institute of Algological Research [Muroran], Hokkaido University, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Johannes Gutenberg - Universität Mainz (JGU), École normale supérieure - Paris (ENS Paris), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Haematology, University of Cambridge [UK] (CAM), Mer et santé (MS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Arizona, The University of Tennessee Health Science Center [Memphis] (UTHSC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), California State University [Los Angeles] (CAL STATE LA), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Systemix Institute, Savelli, Bruno, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), J. Craig Venter Institute, 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), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), 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-PSL), 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), Adaptation et diversité en milieu marin (AD2M), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Charles University [Prague] (CU), Hokkaido University [Sapporo, Japan], Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Université Paris sciences et lettres (PSL), 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 Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), 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 Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: 0106 biological sciences, Lineage (evolution), Molecular Sequence Data, Phaeophyta, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Algae, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Botany, BIOLOGIE CELLULAIRE, Animals, 14. Life underwater, [SDV.BDD]Life Sciences [q-bio]/Development Biology, flore marine, Phylogeny, Organism, ComputingMilieux_MISCELLANEOUS, phéophycées, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Ectocarpus siliculosus, Algal Proteins, Eukaryota, Pigments, Biological, Ectocarpus, 15. Life on land, biology.organism_classification, Biological Evolution, Brown algae, Multicellular organism, Evolutionary biology, algues brunes, Biologie, Signal Transduction, 010606 plant biology & botany
Abstract: Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. © 2010 Macmillan Publishers Limited. All rights reserved.
Published: 2010
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9. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

Author: Francis Martin, Annegret Kohler, Claude Murat, Raffaella Balestrini, Pedro M. Coutinho, Olivier Jaillon, Barbara Montanini, Emmanuelle Morin, Benjamin Noel, Riccardo Percudani, Bettina Porcel, Andrea Rubini, Antonella Amicucci, Joelle Amselem, Véronique Anthouard, Sergio Arcioni, François Artiguenave, Jean-Marc Aury, Paola Ballario, Angelo Bolchi, Andrea Brenna, Annick Brun, Marc Buée, Brandi Cantarel, Gérard Chevalier, Arnaud Couloux, Corinne Da Silva, France Denoeud, Sébastien Duplessis, Stefano Ghignone, Benoît Hilselberger, Mirco Iotti, Benoît Marçais, Antonietta Mello, Michele Miranda, Giovanni Pacioni, Hadi Quesneville, Claudia Riccioni, Roberta Ruotolo, Richard Splivallo, Vilberto Stocchi, Emilie Tisserant, Arturo Roberto Viscomi, Alessandra Zambonelli, Elisa Zampieri, Bernard Henrissat, Marc-Henri Lebrun, Francesco Paolocci, Paola Bonfante, Simone Ottonello, Patrick Wincker, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Architecture et fonction des Macromolécules Biologiques - UMR 6098 (AFMB), Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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, Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Parma [Parme, Italie], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Consiglio Nazionale delle Ricerche [Milano] (CNR), Dipartimento di Scienze Biomolecolari Universita di Urbino (DISB), Università degli Studi di Urbino 'Carlo Bo', Institut National de la Recherche Agronomique (INRA), Génomique métabolique (UMR 8030), 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 Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Dipartimento di Genetica e Biologia Molecolare, Università degli Studi di Roma 'La Sapienza' [Rome], Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Università degli Studi di Bologna, Dipartimento di Biologia Vegetale, Università degli studi di Torino (UNITO), Dipartimento di Biologia di Base ed Applicata, Aquila University, Università degli Studi dell'Aquila [L'Aquila] (UNIVAQ.IT), Unité de Recherche Génomique Info (URGI), CNR IGV, Consiglio Nazionale delle Ricerche (CNR), University of Goettingen, Consiglio Nazionale delle Ricerche [Torino] (CNR), 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), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Istituto di Scienze e Tecnologie Molecolari = Institute of Molecular Science and Technologies (ISTM-CNR [Perugia - Milano]), ANR-06-BLAN-0399,FungEffector,A genome-wide survey of secreted proteins as effectors of symbiosis and pathogenicity in plant-associated fungi(2006), European Project: 33958,EVOLTREE, Martin, Francis, Murat-Furminieux, Claude, Martin F., Kohler A., Murat C., Balestrini R., Coutinho P.M., Jaillon O., Montanini B., Morin E., Noel B., Percudani R., Porcel B., Rubini A., Amicucci A., Amselem J., Anthouard V., Arcioni S., Artiguenave F., Aury J.M., Ballario P., Bolchi A., Brenna A., Brun A., Buée M., Cantarel B., Chevalier G., Couloux A., Da Silva C., Denoeud F., Duplessis S., Ghignone S., Hilselberger B., Iotti M., Mello M., Miranda M., Pacioni G., Quesneville H., Riccioni C., Ruotolo R., Splivallo R., Stocchi V., Tisserant E., Viscomi A.R., Zambonelli A., Zampieri E., Henrissat B., Lebrun M.H., Paolocci F., Bonfante P., Ottonello S., Wincker P., Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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), Università degli studi di Parma = University of Parma (UNIPR), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Università degli studi di Torino = University of Turin (UNITO), Università degli Studi dell'Aquila = University of L'Aquila (UNIVAQ), Georg-August-University = Georg-August-Universität Göttingen, Centre National de la Recherche Scientifique (CNRS)-Université de Provence - Aix-Marseille 1, University of Parma = Università degli studi di Parma [Parme, Italie], Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), 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), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Università degli Studi dell'Aquila (UNIVAQ), University of Göttingen - Georg-August-Universität Göttingen, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), 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), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Tuber melanosporum, tuber, ectomycorrhizal fungi, TRUFFE NOIRE DU PERIGORD, [SDV]Life Sciences [q-bio], Genes, Fungal, Molecular Sequence Data, TRUFFE BLANCHE DU PIEMONT, Carbohydrates, Genomics, Haploidy, 01 natural sciences, Genome, Ectosymbiosis, Evolution, Molecular, 03 medical and health sciences, truffe, Symbiosis, Ascomycota, Tuber aestivum, champignon comestible, Fruiting Bodies, Fungal, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, Truffle, biology, génome, Fungal genetics, Sequence Analysis, DNA, biology.organism_classification, DNA Transposable Elements, fungal genoma, Genome, Fungal, europe, symbiose, Sulfur, 010606 plant biology & botany
Abstract: Letter; International audience; The Périgord black truffle ($Tuber\ melanosporum$ Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of $T.\ melanosporum$ is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal $Laccaria\ bicolor$, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of $T.\ melanosporum$, which at $\sim$125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for $\sim$58% of the genome. In contrast, this genome only contains $\sim$7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that $T.\ melanosporum$ degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both $L.\ bicolor$ and $T.\ melanosporum$, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis $-$'the symbiosis toolbox'$-$ evolved along different ways in ascomycetes and basidiomycetes
Published: 2010
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10. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

Author: Claude Scarpelli, Patrick Wincker, Jean-Marc Aury, Gaelle Samson, Odile Rogier, Julie Poulain, Véronique Anthouard, François Artiguenave, Valérie Barbe, Corinne Cruaud, Sophie Mangenot, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: alignement de séquences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, lcsh:QH426-470, lcsh:Biotechnology, Genomics, Biotechnologies, Computational biology, Biology, DNA sequencing, Computational and Statistical Genetics, procaryote, Contig Mapping, 03 medical and health sciences, lcsh:TP248.13-248.65, séquençage à haut débit, Genetics, Massively parallel, Throughput (business), Gene Library, 030304 developmental biology, Comparative genomics, 0303 health sciences, 030306 microbiology, assemblage bioinformatique, Computational genomics, Computational Biology, Sequence Analysis, DNA, séquençage nouvelle génération, lcsh:Genetics, séquençage du génome, Genome, Bacterial, Research Article, Biotechnology, Personal genomics
Abstract: Background Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been estimated to yield assemblies with more problematic features than the standard method. These problems are of a different nature depending on the techniques used. So, an appropriate mix of technologies may help resolve most difficulties, and eventually provide assemblies of high quality without requiring any Sanger-based input. Results We compared assemblies obtained using Sanger data with those from different inputs from New Sequencing Technologies. The assemblies were systematically compared with a reference finished sequence. We found that the 454 GSFLX can efficiently produce high continuity when used at high coverage. The potential to enhance continuity by scaffolding was tested using 454 sequences from circularized genomic fragments. Finally, we explore the use of Solexa-Illumina short reads to polish the genome draft by implementing a technique to correct 454 consensus errors. Conclusion High quality drafts can be produced for small genomes without any Sanger data input. We found that 454 GSFLX and Solexa/Illumina show great complementarity in producing large contigs and supercontigs with a low error rate.
Published: 2008
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11. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

Author: Graziano Pesole, Benjamin Noel, François Artiguenave, Alberto Policriti, Federica Cattonaro, Alessandro Vezzi, Delphine Jublot, Valérie Laucou, Michel Gouyvenoux, Eléonore Durand, Didier Merdinoglu, Cristian Del Fabbro, Giorgio Valle, Isabelle Le Clainche, Michael Alaux, Irena Juman, Erica Mica, Béatrice Segurens, Alberto Casagrande, Claude Scarpelli, Massimo Delledonne, Gabriele Di Gaspero, Jean-Marc Aury, David S. Horner, Marco Moroldo, M. Enrico Pè, Philippe Hugueney, Mario Pezzotti, Michel Caboche, Anne-Françoise Adam-Blondon, Véronique Anthouard, Nicola Vitulo, Alain Lecharny, Alain Billault, Virginie Vico, Olivier Jaillon, Christian Clepet, Sébastien Aubourg, Michele Morgante, Jean Weissenbach, Patrick Wincker, Nathalie Choisne, Aurélie Canaguier, Corinne Dasilva, Edgardo Ugarte, Philippe Chatelet, Clémence Bruyère, Vincent Dumas, Sophie Paillard, Fabrice Legeai, Nicoletta Felice, Simone Scalabrin, G Malacrida, Julie Poulain, Francis Quetier, Claire Jubin, 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), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Dipartimento di Matematica e Informatica - Universita Udine (DIMI), Università degli Studi di Udine - University of Udine [Italie], Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), CRIBI (CRIBI), Università degli Studi di Padova = University of Padua (Unipd), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano = University of Milan (UNIMI), Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Istituto Tecnologie Biomediche, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Dipartimento Scientifico e Tecnologico (DST), Università degli studi di Verona = University of Verona (UNIVR), Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, VIGNA-CRA Initiative (VIGNA-CRA INITIATIVE), Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, 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), Universita degli Studi di Padova, Università degli Studi di Milano [Milano] (UNIMI), Università degli studi di Bari Aldo Moro (UNIBA), Consiglio Nazionale delle Ricerche [Roma] (CNR), University of Verona (UNIVR), 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), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Università degli studi di Milano [Milano], Università degli studi di Bari, Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Università degli Studi di Verona, O., Jaillon, J., Aury, B., Noel, A., Policriti, C., Clepet, Casagrande, Alberto, N., Choisne, S., Aubourg, N., Vitulo, C., Jubin, A., Vezzi, F., Legeai, P., Hugueney, C., Dasilva, D., Horner, E., Mica, D., Jublot, J., Poulain, C., Bruyère, A., Billault, B., Seguren, M., Gouyvenoux, E., Ugarte, F., Cattonaro, V., Anthouard, V., Vico, C., DEL FABBRO, M., Alaux, G., DI GASPERO, V., Duma, N., Felice, S., Paillard, I., Juman, M., Moroldo, S., Scalabrin, A., Canaguier, I., LE CLAINCHE, G., Malacrida, E., Durand, G., Pesole, V., Laucou, P., Chatelet, D., Merdinoglu, M., Delledonne, M., Pezzotti, A., Lecharny, C., Scarpelli, F., Artiguenave, M. E., Pè, G., Valle, M., Morgante, M., Caboche, A., ADAM BLONDON, J., Weissenbach, F., Quétier, and P., Wincker
Subjects: 0106 biological sciences, genotype, Arabidopsis, POLYPLOIDY, adaptation, 01 natural sciences, Genome, RNA, Transfer, Gene duplication, plant genomics, plant genome evolution, Sequencing, Vitis, vitis vinifera, genome sequencing, 2. Zero hunger, Genetics, Plant evolution, 0303 health sciences, Multidisciplinary, food and beverages, Exons, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Paleopolyploidy, Populus, RNA, Plant, ARABIDOPSIS-THALIANA, DNA-SEQUENCE, GENE, DUPLICATION, MAP, IDENTIFICATION, EVOLUTION, DNA, Intergenic, vine, Genome, Plant, assembly, Bioinformatics, Molecular Sequence Data, Genomics, Biology, Genes, Plant, Monocotyledon, DNA sequencing, Evolution, Molecular, Polyploidy, 03 medical and health sciences, evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, angiosperm, genome, 030304 developmental biology, Whole genome sequencing, fungi, Oryza, Sequence Analysis, DNA, 15. Life on land, chronology, Introns, grapevine, MicroRNAs, polyploidy, Karyotyping, vitis classification, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract: International audience; The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Published: 2007
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12. Genome sequence of the plant pathogen Ralstonia solanacearum

Author: Jean Weissenbach, Patricia Siguier, Marcel Salanoubat, Nathalie Choisne, J. C. Camus, M. Lavie, C. Claudel-Renard, Cedric Robert, Philippe Brottier, Patrick Wincker, Sophie Mangenot, A. Billault, François Artiguenave, Manuel Levy, Michael Chandler, M. Whalen, Christine Gaspin, Laurence Cattolico, Thomas Schiex, Stéphane Genin, Sébastien Cunnac, Christian Boucher, William Saurin, Annick Moisan, Jérôme Gouzy, Patricia Thebault, Matthieu Arlat, N. Demange, Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, MESH: Sequence Analysis, DNA, Molecular Sequence Data, MESH: Gram-Negative Aerobic Rods and Cocci, Genomics, MESH: Biological Evolution, Biology, MESH: Virulence, MESH: Genome, Bacterial, Genome, 03 medical and health sciences, RALSTONIA SOLANACEARUM, Bacterial Proteins, Solanum lycopersicum, MESH: Lycopersicon esculentum, Gene, MESH: Bacterial Proteins, 030304 developmental biology, Genomic organization, Genetics, Whole genome sequencing, 0303 health sciences, Ralstonia solanacearum, Multidisciplinary, MESH: Molecular Sequence Data, Virulence, 030306 microbiology, MESH: Genomics, food and beverages, Sequence Analysis, DNA, biology.organism_classification, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gram-Negative Aerobic Rods and Cocci, Mobile genetic elements, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial
Abstract: 47 refs.; International audience; Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.
Published: 2002
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13. Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum

Author: Cécile Neuvéglise, François Artiguenave, Pascal Durrens, Elisabeth Bon, Serge Casaregola, Patrick Wincker, Michel Aigle, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, Retroelements, Saccharomyces cerevisiae, Centromere, Molecular Sequence Data, Biophysics, Saccharomyces bayanus, Introgression, Translocation, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Biochemistry, 03 medical and health sciences, Contig Mapping, Saccharomyces, Ascomycota, Structural Biology, Gene Order, Genetics, ORFS, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Synteny, 0303 health sciences, 030306 microbiology, Cell Biology, Sequence Analysis, DNA, Ty, biology.organism_classification, Open reading frame, Chromosomes, Fungal, Genome, Fungal
Abstract: Saccharomyces bayanus var. uvarum investigated here is the species closest to Saccharomyces cerevisiae. Random sequence tags (RSTs) allowed us to identify homologues to 2789 open reading frames (ORFs) in S. cerevisiae, ORFs duplicated in S. uvarum but not in S. cerevisiae, centromeres, tRNAs, homologues of Ty1/2 and Ty4 retrotransposons, and a complete rDNA repeat. Only 13 RSTs seem to be homologous to sequences in other organisms but not in S. cerevisiae. As the synteny between the two species is very high, cases in which synteny is lost suggest special mechanisms of genome evolution. The corresponding RSTs revealed that S. uvarum can exist without any S. cerevisiae DNA introgression. Accession numbers are from AL397139 to AL402278 in the EMBL databank.
Published: 2001

14. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes

Author: Elisabeth Bon, Jean Weissenbach, William Saurin, Patrick Wincker, Micheline Wésolowski-Louvel, Michel Termier, Claire Toffano-Nioche, Michel Aigle, Jacky de Montigny, Philippe Brottier, Bertrand Llorente, Andrée Lépingle, Claude Gaillardin, Alain Malpertuy, Pascal Durrens, Serge Casaregola, Jean-Luc Souciet, Monique Bolotin-Fukuhara, Serge Potier, Guillemette Duchateau-Nguyen, François Artiguenave, Odile Ozier-Kalogeropoulos, Fredj Tekaia, Bernard Dujon, Gaëlle Blandin, Cécile Neuvéglise, Laboratoire de Génétique Moléculaire et Cellulaire (INRA UMR216-URA1925), Institut National de la Recherche Agronomique (INRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Unité de Microbiologie et génétique (UMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de génétique moléculaire et cellulaire, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Speciation, Biodiversity, MESH: Research Support, Non-U.S. Gov't, Biochemistry, MESH: Gene Amplification, MESH: Variation (Genetics), MESH: Yeast, Structural Biology, Yeasts, Gene cluster, MESH: Phylogeny, Phylogeny, Genetics, 0303 health sciences, biology, MESH: Genomics, MESH: Comparative Study, Genomics, MESH: Saccharomyces cerevisiae, Horizontal gene transfer, MESH: Fungal Proteins, Genes, Fungal, Saccharomyces cerevisiae, Biophysics, MESH: Ascomycota, MESH: Sequence Homology, Nucleic Acid, Fungal Proteins, 03 medical and health sciences, MESH: Software, Ascomycota, Species Specificity, Phylogenetics, Sequence Homology, Nucleic Acid, Gene family, MESH: Species Specificity, Molecular Biology, Gene, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 030306 microbiology, Gene Amplification, Genetic Variation, Cell Biology, 15. Life on land, biology.organism_classification, Yeast, MESH: Genes, Fungal, Software, Pathway
Abstract: We explored the biological diversity of hemiascomycetous yeasts using a set of 22 000 newly identified genes in 13 species through BLASTX searches. Genes without clear homologue in Saccharomyces cerevisiae appeared to be conserved in several species, suggesting that they were recently lost by S. cerevisiae. They often identified well-known species-specific traits. Cases of gene acquisition through horizontal transfer appeared to occur very rarely if at all. All identified genes were ascribed to functional classes. Functional classes were differently represented among species. Species classification by functional clustering roughly paralleled rDNA phylogeny. Unequal distribution of rapidly evolving, ascomycete-specific, genes among species and functions was shown to contribute strongly to this clustering. A few cases of gene family amplification were documented, but no general correlation could be observed between functional differentiation of yeast species and variations of gene family sizes. Yeast biological diversity seems thus to result from limited species-specific gene losses or duplications, and for a large part from rapid evolution of genes and regulatory factors dedicated to specific functions.
Published: 2000
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15. Genomic exploration of the hemiascomycetous yeasts: 6. Saccharomyces exiguus

Author: François Artiguenave, Serge Casaregola, Patrick Wincker, Andrée Lépingle, Claude Gaillardin, Elisabeth Bon, Cécile Neuvéglise, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mitochondrial DNA, Genes, Fungal, Molecular Sequence Data, Saccharomyces cerevisiae, Gene Dosage, Biophysics, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Saccharomyces, 03 medical and health sciences, Ascomycota, Structural Biology, Gene Duplication, Gene Order, Genetics, Homologous chromosome, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Duplicated gene, biology, 030306 microbiology, Genomics, Cell Biology, biology.organism_classification, Open reading frame, genomic DNA, DNA Transposable Elements, Genome, Fungal, Sequence Alignment
Abstract: Random sequence tags were obtained from a genomic DNA library of Saccharomyces exiguus. The mitochondrial genome appeared to be at least 25.7 kb in size, with a different organization compared to Saccharomyces cerevisiae. An unusual putative 953 bp long terminal repeated element associated to Ty3 was found. A set of 1451 genes was identified homologous to S. cerevisiae open reading frames. Only five genes were identified outside the S. cerevisiae taxon, confirming that S. exiguus is phylogenetically closely related to S. cerevisiae. Unexpectedly, numerous duplicated genes were found whereas they are unique in S. cerevisiae. The sequences are deposited at EMBL under the accession numbers: AL407377–AL409955.
Published: 2000

16. Genomic exploration of the hemiascomycetous yeasts: 7. Saccharomyces servazzii

Author: Cécile Neuvéglise, François Artiguenave, Andrée Lépingle, Elisabeth Bon, Claude Gaillardin, Patrick Wincker, Serge Casaregola, Huu-Vang Nguyen, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transposable element, Retroelements, Molecular Sequence Data, Saccharomyces cerevisiae, Biophysics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Saccharomyces, Genome, Plasmid, Homology (biology), Fungal Proteins, 03 medical and health sciences, Ascomycota, Structural Biology, Gene Duplication, Genetics, Humans, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Kluyveromyces lactis, 0303 health sciences, Sequence Homology, Amino Acid, biology, 030306 microbiology, Nuclear Proteins, Sequence Analysis, DNA, Cell Biology, Spliceosomal intron, biology.organism_classification, Introns, Mitochondrial DNA, Schizosaccharomyces pombe, Spliceosomes, Saccharomyces sensu lato, Genome, Fungal, Plasmids
Abstract: The genome of Saccharomyces servazzii was analyzed with 2570 random sequence tags totalling 2.3 Mb. BLASTX comparisons revealed a minimum of 1420 putative open reading frames with significant homology to Saccharomyces cerevisiae (58% aa identity on average), two with Schizosaccharomyces pombe and one with a human protein, confirming that S. servazzii is closely related to S. cerevisiae. About 25% of the S. servazzii genes were identified, assuming that the gene complement is identical in both yeasts. S. servazzii carries very few transposable elements related to Ty elements in S. cerevisiae. Most of the mitochondrial genes were identified in eight contigs altogether spanning 25 kb for a predicted size of 29 kb. A significant match with the Kluyveromyces lactis linear DNA plasmid pGKL-1 encoded RF4 killer protein suggests that a related plasmid exists in S. servazzii. The sequences have been deposited with EMBL under the accession numbers AL402279–AL404848.
Published: 2000

17. Genomic exploration of the hemiascomycetous yeasts: 14. Debaryomyces hansenii var. hansenii

Author: Patrick Wincker, Cécile Neuvéglise, Elisabeth Bon, Huu-Vang Nguyen, François Artiguenave, Claude Gaillardin, Andrée Lépingle, Serge Casaregola, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transposable element, Molecular Sequence Data, Saccharomyces cerevisiae, Biophysics, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Genome, Homology (biology), Fungal Proteins, 03 medical and health sciences, Ascomycota, RNA, Transfer, Structural Biology, Gene Duplication, Debaryomyces hansenii, Genetics, Non-conventional yeast, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Ribosomal DNA, 0303 health sciences, biology, Contig, 030306 microbiology, Nuclear Proteins, Cell Biology, biology.organism_classification, Mitochondrial DNA, DNA Transposable Elements, Genome, Fungal
Abstract: By analyzing 2830 random sequence tags (RSTs), totalling 2.7 Mb, we explored the genome of the marine, osmo- and halotolerant yeast, Debaryomyces hansenii. A contig 29 kb in length harbors the entire mitochondrial genome. The genes encoding Cox1, Cox2, Cox3, Cob, Atp6, Atp8, Atp9, several subunits of the NADH dehydrogenase complex 1 and 11 tRNAs were unambiguously identified. An equivalent number of putative transposable elements compared to Saccharomyces cerevisiae were detected, the majority of which are more related to higher eukaryote copia elements. BLASTX comparisons of RSTs with databases revealed at least 1119 putative open reading frames with homology to S. cerevisiae and 49 to other genomes. Specific functions, including transport of metabolites, are clearly over-represented in D. hansenii compared to S. cerevisiae, consistent with the observed difference in physiology of the two species. The sequences have been deposited with EMBL under the accession numbers AL436045–AL438874.
Published: 2000

18. Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica

Author: François Artiguenave, Cécile Neuvéglise, Elisabeth Bon, Andrée Lépingle, Chantal Feynerol, Serge Casaregola, Claude Gaillardin, Patrick Wincker, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transposable element, Molecular Sequence Data, Saccharomyces cerevisiae, Biophysics, Functional classification, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Genome, Homology (biology), Fungal Proteins, 03 medical and health sciences, Structural Biology, Gene Duplication, Yeasts, Genetics, Molecular Biology, Gene, Non-conventional yeast, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Sequence Homology, Amino Acid, biology, 030306 microbiology, Yarrowia, Cell Biology, biology.organism_classification, Mitochondrial DNA, GENOMIQUE, Ion homeostasis, DNA Transposable Elements, Genome, Fungal
Abstract: A total of 4940 random sequence tags of the dimorphic yeast Yarrowia lipolytica , totalling 4.9 Mb, were analyzed. BLASTX comparisons revealed at least 1229 novel Y. lipolytica genes 1083 genes having homology with Saccharomyces cerevisiae genes and 146 with genes from various other genomes. This confirms the rapid sequence evolution assumed for Y. lipolytica . Functional analysis of newly discovered genes revealed that several enzymatic activities were increased compared to S. cerevisiae , in particular, transport activities, ion homeostasis, and various metabolism pathways. Most of the mitochondrial genes were identified in contigs spanning more than 47 kb. Matches to retrotransposons were observed, including a S. cerevisiae Ty3 and a LINE element. The sequences have been deposited with EMBL under the accession numbers AL409956 – AL414895 .
Published: 2000

19. A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

Author: Betina M. Porcel, Patrick Wincker, Philippe Grellier, François Artiguenave, Sébastien Charneau, Eric Maréchal, Isabelle Florent, Laurent Brehelin, Corinne Da Silva, Elodie Guillaume, Olivier Gascuel, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-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), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: alignement de séquences, Genes, Protozoan, Protozoan Proteins, polymorphisme, Genome, polymorphism, Genomic library, Genetics, Expressed Sequence Tags, 0303 health sciences, Expressed sequence tag, expression protein, 030302 biochemistry & molecular biology, Exons, Subtelomere, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], protéine, parasite, Bio-informatique, DNA microarray, RNA, Protozoan, Biotechnology, Research Article, lcsh:QH426-470, Bioinformatics, lcsh:Biotechnology, Molecular Sequence Data, Plasmodium falciparum, Schizonts, Biology, 03 medical and health sciences, lcsh:TP248.13-248.65, parasitic diseases, gene, genome, Human parasite, sequence alignment, Apicomplexa, Animals, Gene, 030304 developmental biology, Gene Library, Polymorphism, Genetic, Models, Genetic, génome, Intron, Sequence Analysis, DNA, Actin cytoskeleton, Introns, lcsh:Genetics, structure génétique, RNA, Ribosomal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Protozoan, Sequence Alignment
Abstract: Background The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and functional assessments of P. falciparum genes and expression, and polymorphic data are further necessary to exploit genomic information to further qualify therapeutic target candidates. Here, we undertook a large scale analysis of a P. falciparum FcB1-schizont-EST library previously constructed by suppression subtractive hybridization (SSH) to study genes expressed during merozoite morphogenesis, with the aim of: 1) obtaining an exhaustive collection of schizont specific ESTs, 2) experimentally validating or correcting P. falciparum gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains. Results A total of 22,125 clones randomly picked from the SSH library were sequenced, yielding 21,805 usable ESTs that were then clustered on the P. falciparum genome. This allowed identification of 243 protein coding genes, including 121 previously annotated as hypothetical. Statistical analysis of GO terms, when available, indicated significant enrichment in genes involved in "entry into host-cells" and "actin cytoskeleton". Although most ESTs do not span full-length gene reading frames, detailed sequence comparison of FcB1-ESTs versus 3D7 genomic sequences allowed the confirmation of exon/intron boundaries in 29 genes, the detection of new boundaries in 14 genes and identification of protein polymorphism for 21 genes. In addition, a large number of non-protein coding ESTs were identified, mainly matching with the two A-type rRNA units (on chromosomes 5 and 7) and to a lower extent, two atypical rRNA loci (on chromosomes 1 and 8), TARE subtelomeric regions (several chromosomes) and the recently described telomerase RNA gene (chromosome 9). Conclusion This FcB1-schizont-EST analysis confirmed the actual expression of 243 protein coding genes, allowing the correction of structural annotations for a quarter of these sequences. In addition, this analysis demonstrated the actual transcription of several remarkable non-protein coding loci: 2 atypical rRNA, TARE region and telomerase RNA gene. Together with other collections of P. falciparum ESTs, usually generated from mixed parasite stages, this collection of FcB1-schizont-ESTs provides valuable data to gain further insight into the P. falciparum gene structure, polymorphism and expression.
Published: 2009
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20. Annotating genomes with massive-scale RNA sequencing

Author: Patrick Wincker, François Artiguenave, Claude Scarpelli, Jean-Marc Aury, Odile Rogier, Giorgio Valle, Olivier Jaillon, Michele Morgante, Benjamin Noel, Corinne Da Silva, Massimo Delledonne, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Verona (UNIVR), Istituto di Genomica Applicata, Universita di Padova, Università degli studi di Verona = University of Verona (UNIVR), and Università degli Studi di Padova = University of Padua (Unipd)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, DNA, Complementary, Sequence analysis, genetic processes, Method, Genomics, Biotechnologies, annotation génomique, Computational biology, Biology, 01 natural sciences, Genome, 03 medical and health sciences, natural sciences, Vitis, Gene, 030304 developmental biology, Comparative genomics, Genetics, 0303 health sciences, Models, Genetic, Sequence Analysis, RNA, Annotating genomes with massive-scale RNA sequencing, séquençage nouvelle génération, ComputingMethodologies_PATTERNRECOGNITION, RNA, Plant, RNA splicing, séquençage adn, Functional genomics, Genome, Plant, 010606 plant biology & botany, Personal genomics
Abstract: A method for de novo genome annotation using high-throughput cDNA sequencing data., Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes and/or splicing events. We present G-Mo.R-Se (Gene Modelling using RNA-Seq), an approach aimed at building gene models directly from RNA-Seq and demonstrate its utility on the grapevine genome.
Published: 2008
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21. Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

Author: Patrick Wincker, François Artiguenave, Andrée Lépingle, Serge Casaregola, Elisabeth Bon, Claude Gaillardin, Cécile Neuvéglise, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: tRNA gene, Molecular Sequence Data, Saccharomyces cerevisiae, Karyotype, Biophysics, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biochemistry, Genome, Fungal Proteins, Open Reading Frames, Saccharomyces, 03 medical and health sciences, chemistry.chemical_compound, Ascomycota, RNA, Transfer, Structural Biology, Genetics, Melibiose, Molecular Biology, Gene, Ribosomal DNA, ComputingMilieux_MISCELLANEOUS, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Cell Biology, biology.organism_classification, Long terminal repeat, Yeast, Open reading frame, chemistry, 13. Climate action, Genome, Fungal
Abstract: The genome of Saccharomyces kluyveri was explored through 2528 random sequence tags with an average length of 981 bp. The complete nuclear ribosomal DNA unit was found to be 8656 bp in length. Sequences homologous to retroelements of the gypsy and copia types were identified as well as numerous solo long terminal repeats. We identified at least 1406 genes homologous to Saccharomyces cerevisiae open reading frames, with on average 58.1% and 72.4% amino acid identity and similarity, respectively. In addition, by comparison with completely sequenced genomes and the SwissProt database, we found 27 novel S. kluyveri genes. Most of these genes belong to pathways or have functions absent from S. cerevisiae , such as the catabolic pathway of purines or pyrimidines, melibiose fermentation, sorbitol utilization, or degradation of pollutants. The sequences are deposited in EMBL under the accession numbers AL404849 – AL407376 .
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22. Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

Author: William Saurin, Cécile Neuvéglise, Bertrand Llorente, Philippe Brottier, Andrée Lépingle, Bernard Dujon, Micheline Wésolowski-Louvel, Serge Casaregola, Monique Bolotin-Fukuhara, Claire Toffano-Nioche, Gaëlle Blandin, Elisabeth Bon, Odile Ozier-Kalogeropoulos, Patrick Wincker, Jean Weissenbach, Alain Malpertuy, François Artiguenave, Pascal Durrens, Michel Aigle, Serge Potier, Claude Gaillardin, Jean-Luc Souciet, Fredj Tekaia, Jacky de Montigny, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, Gene duplication, Genes, Fungal, Saccharomyces cerevisiae, Biophysics, Gene redundancy, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biochemistry, Genome, Evolution, Molecular, 03 medical and health sciences, Ascomycota, Structural Biology, Gene cluster, Genetics, Gene family, Molecular Biology, Gene, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Base Sequence, Models, Genetic, biology, Gene deletion, 030302 biochemistry & molecular biology, Genetic Variation, Cell Biology, Telomere, biology.organism_classification, Paralogue, Multigene Family, Orthologue, Genome, Fungal
Abstract: We have evaluated the degree of gene redundancy in the nuclear genomes of 13 hemiascomycetous yeast species. Saccharomyces cerevisiae singletons and gene families appear generally conserved in these species as singletons and families of similar size, respectively. Variations of the number of homologues with respect to that expected affect from 7 to less than 24% of each genome. Since S. cerevisiae homologues represent the majority of the genes identified in the genomes studied, the overall degree of gene redundancy seems conserved across all species. This is best explained by a dynamic equilibrium resulting from numerous events of gene duplication and deletion rather than by a massive duplication event occurring in some lineages and not in others.
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22 results on '"François Artiguenave"'

1. 3-Keto-5-aminohexanoate Cleavage Enzyme

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

3. In Vitro and In Vivo Modulation of Alternative Splicing by the Biguanide Metformin

4. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

5. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining

6. Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

7. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

8. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

9. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

10. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

11. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

12. Genome sequence of the plant pathogen Ralstonia solanacearum

13. Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum

14. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes

15. Genomic exploration of the hemiascomycetous yeasts: 6. Saccharomyces exiguus

16. Genomic exploration of the hemiascomycetous yeasts: 7. Saccharomyces servazzii

17. Genomic exploration of the hemiascomycetous yeasts: 14. Debaryomyces hansenii var. hansenii

18. Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica

19. A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

20. Annotating genomes with massive-scale RNA sequencing

21. Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

22. Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

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22 results on '"François Artiguenave"'

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