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29 results on '"Jerome Gouzy"'

1. Diversity and Mechanisms of Genomic Adaptation in Penicillium

Author

Jeanne Ropars, Ricardo Rodriguez de la Vega, Manuela López-Villavicencio, Jerome Gouzy, Joëlle Dupont, Dominique Swennen, Emilie Dumas, Tatiana Giraud, Antoine Branca, Université Paris-Sud - Paris 11 (UP11), Centre National de la Recherche Scientifique (CNRS), Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AgroParisTech, Univ. Paris-Sud, Université Paris-Saclay, Ronald P. de Vries, Isabelle Benoit Gelber, Mikael Rørdam Andersen, European Project: 309403,EC:FP7:ERC,ERC-2012-StG_20111109,GENOMEFUN(2013), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
2. Zero hunger, 0303 health sciences, 03 medical and health sciences, 030306 microbiology, [SDV]Life Sciences [q-bio], food and beverages, 15. Life on land, 030304 developmental biology
Abstract

International audience; Penicillium is a diverse fungal genus with hundreds of species occurring worldwide in various substrates, from soil to food, and with various lifestyles, from necrotrophic pathogenicity to endophytic mutualism. Several species are important for human affairs, being widely used in industry, such as the penicillin-producer P. rubens, the two cheese starters P. camemberti and P. roqueforti, and the mould used for fermenting sausages, P. nalgiovense. Other species are food spoilers that produce harmful mycotoxins or cause damages in fruit crops. Currently , 30 genomes of Penicillium belonging to 18 species are available. In this chapter, we reconstruct a phylogenetic tree based on available Penicillium genomes and outline the main features of the genomes, such as gene and transposable element content. We then review the recent advances that the available genomic and transcriptomic resources in the Penicillium genus have allowed regarding our understanding of the genomic processes of adaptation, including changes in gene content, expression and strikingly frequent and recent horizontal gene transfers. In addition, we summarize recent studies using genetic markers on the level of genetic diversity, mode of reproduction and population structure within Penicillium species. Overall, the Penicillium genus appears a highly suitable model for studying the mechanisms of adaptation. Introduction Penicillium is a diverse fungal genus with 354 accepted species today (Visagie et al., 2014b), occurring worldwide in various substrates, from soil to food. Their lifestyles also cover a broad range, from necrotrophic pathogenicity to endophytic mutualism, although most are saprotrophs. As a consequence of these ecological niches, many Penicillium species have important economic and social relevance for human populations. Several species are widely used in industry, such as the penicillin-producer P. rubens, the two cheese starters P. camem-berti and P. roqueforti, and the mould used for fermenting sausages, P. nalgiovense (Bernáldez et al., 2013). Other species cause damages and yield loss in fruit crops, e.g. P. digitatum and P. italicum, while others are a concern for food safety because of their production of myco-toxins, such as patulin (Eckert and Eaks, 1989; McCallum et al., 2002).

Published
2016

2. Génétique et génomique du pois : what else ?

Author

Judith Burstin, Tayeh, Nadim N., Anthony Klein, Virginie Bourion, Jonathan Kreplak, Françoise Jacquin, Susete Alves Carvalho, Christelle Aluome, Sebastien Carrere, Jerome Gouzy, Corinne Cruaud, Gérard Duc, Pascal Gamas, Brunel, Dominique D., Matthieu Falque, Marie-Christine Le Paslier, Patrick Wincker, Aubert, Gregoire G., Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Bayer Cropscience, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Société Nationale d'Horticulture de France (SNHF). FRA., Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
pois, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, génétique, génomique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

3. Pea genomic tools for functional and structural approaches

Author

Nadim Tayeh, Susete Alves Carvalho, Christelle Aluome, Sébastien Carrere, Jonathan Kreplak, Anthony Klein, Matthieu Falque, Corinne Cruaud, Pauline Salloignon, Caroline Truntzer, Jerome Gouzy, Patrick Wincker, Marie-Christine Le Paslier, Dominique Brunel, Gregoire Aubert, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Bayer Cropscience, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Masaryk University. CZE., Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
genomic, [SDV]Life Sciences [q-bio], pea, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

BAP Geapsi; International audience

Published
2015

4. Use of translational genomics to identify genes important for legume seed filling

Author

Mélanie Noguero, Erfurth, Isabelle D., Christine Le Signor, Vanessa Vernoud, Jérôme Verdier, Gregoire Aubert, Julia Buitink, Jerome Gouzy, Jean-Marie Prosperi, Thierry Huguet, Judith Burstin, Karine Gallardo, Richard Thompson, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Plant Biology Division, The Samuel Roberts Noble Foundation, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), École nationale supérieure agronomique de Toulouse [ENSAT], and ProdInra, Migration

Subjects
translational genomics, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, fungi, legume seed filling, food and beverages, medicago truncatula, [SDV.IDA] Life Sciences [q-bio]/Food engineering, model species, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, [SDV.BDD] Life Sciences [q-bio]/Development Biology, [SDV.IDA]Life Sciences [q-bio]/Food engineering, sequencing genome, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

International audience; Translational genomics, i.e., the transfer of genetic information from model species to cultivated crops, is on the brink of revolutionizing plant breeding. The recent publication of genomic sequences for several cultivated legumes is also accelerating this process. For pea, recent highthroughput RNA sequencing, and the prospect of a genome sequencing project, will further accelerate the transfer of information from the Medicago truncatula model to the cultivated crop. We have been using genomics approaches with Medicago as a tool to identify key genes determining seed yield and composition in closely related legumes. Analyses of the proteome and transcriptome of the component tissues of the developing seed revealed extensive compartmentalization of gene expression and metabolic activities. Using a TF (Transcription Factor) qRT-PCR platform and the Affymetrix Gene Chip, TFs specific for each seed tissue were identified, along with putative target genes. These TFs have been located on the M. truncatula genetic map and correlations between map positions of TF loci and QTLs for protein quantities and other seed phenotypes were detected. These correlations can be recently confirmed in numerous cases by the existence of similar QTLs at syntenic positions in pea. Two genes, both specifically expressed in the developing endosperm, have received particular attention. One of the genes encodes a DOF class transcription factor, whose mutant phenotype severely affects endosperm development. The second gene encodes an endosperm-specific subtilase (SBT1.1), which affects final seed weight. MiRNAs constitute another level of gene regulation whose importance in the developing seed is beginning to become apparent. We have recently started to compare the sRNA profiles of developing M. truncatula and pea seeds and preliminary results will be presented.

Published
2013

5. Development of genomic resources for Medicago truncatula and related legume crops

Author

Frederic Debellé, Marion Verdenaud, Anne-Marie Dudez, Nicolas Samson, Olivier Saurat, Chrystel Gibelin, Philippe Bardou, Céline Noirot, Emmanuel Courcelle, Erika Sallet, Sebastien Carrere, Pascal Gamas, Jerome Gouzy, Thomas Schiex, Bernadette Julier, Ghislaine Magdelenat, Valérie Barbe, Sylvie Samain, Nathalie CHOISNE, Béatrice Ségurens, Stéphanie Fouteau, Arnaud Couloux, Agnès Viollet, Anne Berger, Claude Carpelli, Patrick Wincker, Jean Weissenbach, Francis Quétier, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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), ANR-06-BLAN-0112 'Seqmedic', ANR 08-GEN-015-001 'SYMbiMICS', Genoplante GPLA06026G, INRA AIP Bioressources 2010 'Seqluz', EU GLIP program, Institut National Polytechnique (Toulouse) (Toulouse INP). Castanet Tolosan, FRA., Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (UBIA), and Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2011

6. The roles if embryo-surrounding tissues in regulating Medicago truncatula seed filling

Author

Mélanie Noguero, Christine Le Signor, Jérôme Verdier, Gregoire Aubert, Udvardi, M. K., Julia Buitink, Jerome Gouzy, Jean-Marie Prosperi, Karine Gallardo Guerrero, Richard Thompson, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, The Samuel Roberts Noble Foundation, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
EMBRYO-SURROUNDING TISSUES, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, MEDICAGO TRUNCATULA, ComputingMilieux_MISCELLANEOUS, SEED FILLING
Abstract

National audience

Published
2011

7. Deciphering the genome structure and paleohistory of Theobroma cacao

Author

Mark Guiltinan, Cristian Chaparro, Florent Murat, John Carlson, Valentin Guignon, Mathias Tahi, Emmanuel Guiderdoni, Thierry Legavre, Olivier Fouet, Erika Sallet, Xavier Sabau, Joseph Moroh Akaza, Francis Quetier, Julie Poulain, Schiex T., Michael Axtell, Bertrand Pitollat, Olivier Panaud, Siela Maximova, Manuel Ruiz, Anne Dievart, Zhaorong Ma, Karina Gramacho, Patrick Wincker, Yolande Roguet, Melissa Kramer, Yufan Zhang, Angélique D’Hont, Stephanie Sidibe-Bocs, Claire Lanaud, Xavier Argout, Maguy Rodier-Goud, Laura Gelley, Spencer Brown, Dominique Brunel, Diogenes Infante, Jerome Salse, Jose Fernandes Barbosa-Neto, Zi Sh, Mickael Bourge, Wolfgang Golser, Ismael Kebe, Jean Marc Aury, Francois Sabot, Aurélie Bérard, Christopher Viot, Xiang Song, Pierre Costet, Gaetan Droc, Dave Kudrna, Jetty Siva Ammiraju, Michel Boccara, Didier Clement, Rod Wing, Jerome Gouzy, Michael Abrouk, Stephan Schuster, Ange Marie Risterucci, Ronan Rivalan, W. Richard McCombie, and Mathilde Allegre

Subjects
General Materials Science
Published
2010
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8. Génétique et post-génomique chez la légumineuse modèle M. truncatula pour disséquer le déterminisme moléculaire de la composition protéique des graines de légumineuses

Author

Karine Gallardo Guerrero, Amandine Bordat, Christine Le Signor, Gregoire Aubert, Delphine Aime, Vincent Savois, Marion Verdenaud, Jerome Gouzy, Jean-Marie Prosperi, Thierry Huguet, Céline Vandecasteele, Julia Buitink, Richard Thompson, Judith Burstin, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiologie Moléculaire des Semences (PMS), Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2009

9. BioWorkFlow: Web Services toolkit and workflow applications evaluation to deploy a confidence network

Author

Marc Wessner, Martin Senger, Franck Samson, Philippe Picouet, François Moreews, Hervé Ménager, Véronique Martin, Sébastien Letort, Catherine Letondal, Mark HOEBEKE, Jerome Gouzy, Jean-François Gibrat, Erwan Corre, Olivier Collin, Sébastien Carrere, Christophe Caron, Pierre Tufféry, Bertrand Néron, Unité de Biologie du développement et biotechnologies (JOUY BIOLOG DEVELOP BIOTECHNOL), Institut National de la Recherche Agronomique (INRA), Physiologie Moléculaire du Transport des Sucres chez les Végétaux (PhyMoTS), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Unité Mathématique Informatique et Génome (MIG), Département Logique des Usages, Sciences sociales et Sciences de l'Information (LUSSI), Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT), Lab-STICC_TB_CID_DECIDE, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Institut Pasteur [Paris] (IP), Laboratoire Statistique et Génome (SG), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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), Bioinformatique génomique et moléculaire ((U 726)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Modélisation mathématique et statistique en biologie et médecine, Ecologie et biologie des interactions (EBI), Institut Mines-Télécom [Paris] (IMT)-Télécom Bretagne-Université européenne de Bretagne - European University of Brittany (UEB), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Unité Mathématique, Informatique et Génome (MIG), Unité de Biologie du développement et biotechnologies ( JOUY BIOLOG DEVELOP BIOTECHNOL ), Institut National de la Recherche Agronomique ( INRA ), Ecologie et biologie des interactions ( EBI ), Université de Poitiers-Centre National de la Recherche Scientifique ( CNRS ), Unité Mathématique Informatique et Génome ( MIG ), Département Logique des Usages, Sciences sociales et Sciences de l'Information ( LUSSI ), Université européenne de Bretagne ( UEB ) -Télécom Bretagne-Institut Mines-Télécom [Paris], Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance ( Lab-STICC ), École Nationale d'Ingénieurs de Brest ( ENIB ) -Université de Bretagne Sud ( UBS ) -Université de Brest ( UBO ) -Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques ( IBNM ), Université de Brest ( UBO ) -Université européenne de Bretagne ( UEB ) -ENSTA Bretagne-Institut Mines-Télécom [Paris]-Centre National de la Recherche Scientifique ( CNRS ) -École Nationale d'Ingénieurs de Brest ( ENIB ) -Université de Bretagne Sud ( UBS ) -Université de Brest ( UBO ) -Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques ( IBNM ), Université de Brest ( UBO ) -Université européenne de Bretagne ( UEB ) -ENSTA Bretagne-Institut Mines-Télécom [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Biological systems and models, bioinformatics and sequences ( SYMBIOSE ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique ( Inria ), Institut national de la recherche agronomique [Toulouse] ( INRA Toulouse ), Laboratoire Statistique et Génome ( SG ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des interactions plantes micro-organismes ( LIPMO ), Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ), Unité Mathématique, Informatique et Génome ( MIG ), Végétaux marins et biomolécules ( UMR7139 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -GOEMAR-Centre National de la Recherche Scientifique ( CNRS ), Bioinformatique génomique et moléculaire, Université Paris Diderot - Paris 7 ( UPD7 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7)

Subjects
[ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2008

10. Evolution of Fusarium tricinctum and Fusarium avenaceum mitochondrial genomes is driven by mobility of introns and of a new type of palindromic microsatellite repeats

Author

Nadia Ponts, Charlotte Gautier, Jérôme Gouzy, Laetitia Pinson-Gadais, Marie Foulongne-Oriol, Christine Ducos, Florence Richard-Forget, Jean-Michel Savoie, Chen Zhao, and Gérard Barroso

Subjects
Group I intron, Homing endonuclease, Lateral transfer, Palindrome, Fusarium tricinctum species complex, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Increased contamination of European and Asian wheat and barley crops with “emerging” mycotoxins such as enniatins or beauvericin, produced by Fusarium avenaceum and Fusarium tricinctum, suggest that these phylogenetically close species could be involved in future food-safety crises. Results The mitochondrial genomes of F. tricinctum strain INRA104 and F. avenaceum strain FaLH27 have been annotated. A comparative analysis was carried out then extended to a set of 25 wild strains. Results show that they constitute two distinct species, easily distinguished by their mitochondrial sequences. The mitochondrial genetic variability is mainly located within the intergenic regions. Marks of variations show they have evolved (i) by Single Nucleotide Polymorphisms (SNPs), (ii) by length variations mediated by insertion/deletion sequences (Indels), and (iii) by length mutations generated by DNA sliding events occurring in mononucleotide (A)n or (T)n microsatellite type sequences arranged in a peculiar palindromic organization. The optionality of these palindromes between both species argues for their mobility. The presence of Indels and SNPs in palindrome neighbouring regions suggests their involvement in these observed variations. Moreover, the intraspecific and interspecific variations in the presence/absence of group I introns suggest a high mobility, resulting from several events of gain and loss during short evolution periods. Phylogenetic analyses of intron orthologous sequences suggest that most introns could have originated from lateral transfers from phylogenetically close or distant species belonging to various Ascomycota genera and even to the Basidiomycota fungal division. Conclusions Mitochondrial genome evolution between F. tricinctum and F. avenaceum is mostly driven by two types of mobile genetic elements, implicated in genome polymorphism. The first one is represented by group I introns. Indeed, both genomes harbour optional (inter- or intra-specifically) group I introns, all carrying putatively functional hegs, arguing for a high mobility of these introns during short evolution periods. The gain events were shown to involve, for most of them, lateral transfers between phylogenetically distant species. This study has also revealed a new type of mobile genetic element constituted by a palindromic arrangement of (A) n and (T) n microsatellite sequences whose presence was related to occurrence of SNPs and Indels in the neighbouring regions.

Published
2020
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11. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Author

Bárbara Hufnagel, André Marques, Alexandre Soriano, Laurence Marquès, Fanchon Divol, Patrick Doumas, Erika Sallet, Davide Mancinotti, Sébastien Carrere, William Marande, Sandrine Arribat, Jean Keller, Cécile Huneau, Thomas Blein, Delphine Aimé, Malika Laguerre, Jemma Taylor, Veit Schubert, Matthew Nelson, Fernando Geu-Flores, Martin Crespi, Karine Gallardo, Pierre-Marc Delaux, Jérôme Salse, Hélène Bergès, Romain Guyot, Jérôme Gouzy, and Benjamin Péret

Subjects
Science
Abstract

White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.

Published
2020
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12. Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

Author

Bruno Le Cam, Dan Sargent, Jérôme Gouzy, Joëlle Amselem, Marie-Noëlle Bellanger, Olivier Bouchez, Spencer Brown, Valérie Caffier, Marie De Gracia, Robert Debuchy, Ludovic Duvaux, Thibaut Payen, Mélanie Sannier, Jason Shiller, Jérôme Collemare, and Christophe Lemaire

Subjects
Venturia, Fusicladium, formae specialis, transposable elements, effectors, apple scab, apple, pear, Genetics, QH426-470
Abstract

The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis. We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.

Published
2019
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13. Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

Author

Olivier Arnaiz, Erwin Van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin de Vanssay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy, and Linda Sperling

Subjects
Ciliate, Cap-Seq, TSS, RNA-Seq, Gene annotation, Autogamy, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. Results We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. Conclusions We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3′ and 5′ UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis regulatory motifs). The P. tetraurelia improved transcriptome resource, gene annotations for P. tetraurelia, P. biaurelia, P. sexaurelia and P. caudatum, and Paramecium-trained EuGene configuration are available through ParameciumDB ( http://paramecium.i2bc.paris-saclay.fr ). TrUC software is freely distributed under a GNU GPL v3 licence ( https://github.com/oarnaiz/TrUC ).

Published
2017
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14. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

Author

Baptiste Mayjonade, Jérôme Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade, and Stéphane Muños

Subjects
DNA extraction, long-read sequencing, PacBio, Biology (General), QH301-705.5
Abstract

De novo sequencing of complex genomes is one of the main challenges for researchers seeking high-quality reference sequences. Many de novo assemblies are based on short reads, producing fragmented genome sequences. Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.

Published
2016
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15. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

Author

Romain Blanc-Mathieu, Laetitia Perfus-Barbeoch, Jean-Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martin-Jimenez, Marc Bailly-Bechet, Philippe Castagnone-Sereno, Jean-François Flot, Djampa K Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yu-Jin Kim-Jo, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, and Etienne G J Danchin

Subjects
Genetics, QH426-470
Abstract

Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.

Published
2017
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16. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

Author

Baptiste Mayjonade, Jérôme Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade, and Stéphane Muños

Subjects
Biology (General), QH301-705.5
Abstract

Protocol Summary Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.

Published
2017
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17. Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum.

Author

Anthony Perrier, Rémi Peyraud, David Rengel, Xavier Barlet, Emmanuel Lucasson, Jérôme Gouzy, Nemo Peeters, Stéphane Genin, and Alice Guidot

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

Experimental evolution of the plant pathogen Ralstonia solanacearum, where bacteria were maintained on plant lineages for more than 300 generations, revealed that several independent single mutations in the efpR gene from populations propagated on beans were associated with fitness gain on bean. In the present work, novel allelic efpR variants were isolated from populations propagated on other plant species, thus suggesting that mutations in efpR were not solely associated to a fitness gain on bean, but also on additional hosts. A transcriptomic profiling and phenotypic characterization of the efpR deleted mutant showed that EfpR acts as a global catabolic repressor, directly or indirectly down-regulating the expression of multiple metabolic pathways. EfpR also controls virulence traits such as exopolysaccharide production, swimming and twitching motilities and deletion of efpR leads to reduced virulence on tomato plants after soil drenching inoculation. We studied the impact of the single mutations that occurred in efpR during experimental evolution and found that these allelic mutants displayed phenotypic characteristics similar to the deletion mutant, although not behaving as complete loss-of-function mutants. These adaptive mutations therefore strongly affected the function of efpR, leading to an expanded metabolic versatility that should benefit to the evolved clones. Altogether, these results indicated that EfpR is a novel central player of the R. solanacearum virulence regulatory network. Independent mutations therefore appeared during experimental evolution in the evolved clones, on a crucial node of this network, to favor adaptation to host vascular tissues through regulatory and metabolic rewiring.

Published
2016
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18. A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum.

Author

Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse, Jérôme Gouzy, and Stéphane Genin

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

Bacterial pathogenicity relies on a proficient metabolism and there is increasing evidence that metabolic adaptation to exploit host resources is a key property of infectious organisms. In many cases, colonization by the pathogen also implies an intensive multiplication and the necessity to produce a large array of virulence factors, which may represent a significant cost for the pathogen. We describe here the existence of a resource allocation trade-off mechanism in the plant pathogen R. solanacearum. We generated a genome-scale reconstruction of the metabolic network of R. solanacearum, together with a macromolecule network module accounting for the production and secretion of hundreds of virulence determinants. By using a combination of constraint-based modeling and metabolic flux analyses, we quantified the metabolic cost for production of exopolysaccharides, which are critical for disease symptom production, and other virulence factors. We demonstrated that this trade-off between virulence factor production and bacterial proliferation is controlled by the quorum-sensing-dependent regulatory protein PhcA. A phcA mutant is avirulent but has a better growth rate than the wild-type strain. Moreover, a phcA mutant has an expanded metabolic versatility, being able to metabolize 17 substrates more than the wild-type. Model predictions indicate that metabolic pathways are optimally oriented towards proliferation in a phcA mutant and we show that this enhanced metabolic versatility in phcA mutants is to a large extent a consequence of not paying the cost for virulence. This analysis allowed identifying candidate metabolic substrates having a substantial impact on bacterial growth during infection. Interestingly, the substrates supporting well both production of virulence factors and growth are those found in higher amount within the plant host. These findings also provide an explanatory basis to the well-known emergence of avirulent variants in R. solanacearum populations in planta or in stressful environments.

Published
2016
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19. Symbiosis-Related Plant Genes Modulate Molecular Responses in an Arbuscular Mycorrhizal Fungus During Early Root Interactions

Author

Pascale M. A. Seddas, Cecilia M. Arias, Christine Arnould, Diederik van Tuinen, Olivier Godfroy, Hassan Aït Benhassou, Jérome Gouzy, Dominique Morandi, Fabrice Dessaint, and Vivienne Gianinazzi-Pearson

Subjects
Microbiology, QR1-502, Botany, QK1-989
Abstract

To gain further insight into the role of the plant genome in arbuscular mycorrhiza (AM) establishment, we investigated whether symbiosis-related plant genes affect fungal gene expression in germinating spores and at the appressoria stage of root interactions. Glomus intraradices genes were identified in expressed sequence tag libraries of mycorrhizal Medicago truncatula roots by in silico expression analyses. Transcripts of a subset of genes, with predicted functions in transcription, protein synthesis, primary or secondary metabolism, or of unknown function, were monitored in spores and germinating spores and during interactions with roots of wild-type or mycorrhiza-defective (Myc–) mutants of M. truncatula. Not all the fungal genes were active in quiescent spores but all were expressed when G. intraradices spores germinated in wild-type M. truncatula root exudates or when appressoria or arbuscules were formed in association with wild-type M. truncatula roots. Most of the fungal genes were upregulated or induced at the stage of appressorium development. Inactivation of the M. truncatula genes DMI1, DMI2/MtSYM2, or DMI3/MtSYM13 was associated with altered fungal gene expression (nonactivation or inhibition), modified appressorium structure, and plant cell wall responses, providing first evidence that cell processes modified by symbiosis-related plant genes impact on root interactions by directly modulating AM fungal activity.

Published
2009
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20. Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing.

Author

Taiadjana M Fortuna, Alodie Snirc, Hélène Badouin, Jérome Gouzy, Sophie Siguenza, Diane Esquerre, Stéphanie Le Prieur, Jacqui A Shykoff, and Tatiana Giraud

Subjects
Medicine, Science
Abstract

Anther-smut fungi belonging to the genus Microbotryum sterilize their host plants by aborting ovaries and replacing pollen by fungal spores. Sibling Microbotryum species are highly specialized on their host plants and they have been widely used as models for studies of ecology and evolution of plant pathogenic fungi. However, most studies have focused, so far, on M. lychnidis-dioicae that parasitizes the white campion Silene latifolia. Microbotryum saponariae, parasitizing mainly Saponaria officinalis, is an interesting anther-smut fungus, since it belongs to a tetrapolar lineage (i.e., with two independently segregating mating-type loci), while most of the anther-smut Microbotryum fungi are bipolar (i.e., with a single mating-type locus). Saponaria officinalis is a widespread long-lived perennial plant species with multiple flowering stems, which makes its anther-smut pathogen a good model for studying phylogeography and within-host multiple infections.Here, based on a generated genome sequence of M. saponariae we developed 6 multiplexes with a total of 22 polymorphic microsatellite markers using an inexpensive and efficient method. We scored these markers in fungal individuals collected from 97 populations across Europe, and found that the number of their alleles ranged from 2 to 11, and their expected heterozygosity from 0.01 to 0.58. Cross-species amplification was examined using nine other Microbotryum species parasitizing hosts belonging to Silene, Dianthus and Knautia genera. All loci were successfully amplified in at least two other Microbotryum species.These newly developed markers will provide insights into the population genetic structure and the occurrence of within-host multiple infections of M. saponariae. In addition, the draft genome of M. saponariae, as well as one of the described markers will be useful resources for studying the evolution of the breeding systems in the genus Microbotryum and the evolution of specialization onto different plant species.

Published
2016
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21. Identification of New Potential Regulators of the Medicago truncatula—Sinorhizobium meliloti Symbiosis Using a Large-Scale Suppression Subtractive Hybridization Approach

Author

Laurence Godiard, Andreas Niebel, Fabienne Micheli, Jérôme Gouzy, Thomas Ott, and Pascal Gamas

Subjects
EST, macroarrays, nodulin, supernodulating mutants, Microbiology, QR1-502, Botany, QK1-989
Abstract

ABSTRACT We set up a large-scale suppression subtractive hybridization (SSH) approach to identify Medicago truncatula genes differentially expressed at different stages of the symbiotic interaction with Sinorhizobium meliloti, with a particular interest for regulatory genes. We constructed 7 SSH libraries covering successive stages from Nod factor signal transduction to S. meliloti infection, nodule organogenesis, and functioning. Over 26,000 clones were differentially screened by two rounds of macroarray hybridizations. In all, 3,340 clones, corresponding to genes whose expression was potentially affected, were selected, sequenced, and ordered into 2,107 tentative gene clusters, including 767 MtS clusters corresponding to new M. truncatula genes. In total, 52 genes encoding potential regulatory proteins, including transcription factors (TFs) and other elements of signal transduction cascades, were identified. The expression pattern of some of them was analyzed by quantitative reverse-transcription polymerase chain reaction in wild-type and in Nod¯ M. truncatula mutants blocked before or after S. meliloti infection. Three genes, coding for TFs of the bHLH and WRKY families and a C2H2 zinc-finger protein, respectively, were found to be upregulated, following S. meliloti inoculation, in the infection-defective mutant lin, whereas the bHLH gene also was expressed in the root-hair-curling mutant hcl. The potential role of these genes in early symbiotic steps is discussed.

Published
2007
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22. Rôle de l'albumen dans le developpement de la graine chez les legumineuses

Author

Mélanie Noguero, Christine Le Signor, Jérome Verdier, Gregoire Aubert, Udvardi, M. K., Julia Buitink, Jerome Gouzy, Jean-Marie Prosperi, Karine Gallardo Guerrero, Richard Thompson, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Plant Biology Division, The Samuel Roberts Noble Foundation, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Medicago truncatula transcriptomique, ComputingMilieux_MISCELLANEOUS, facteur de transcription DOF
Abstract

National audience

23. Use of translational genomics to identify genes important for legume seed development

Author

Karine Gallardo, Erfurth, Isabelle D., Christine Le Signor, Vanessa Vernoud, Gregoire Aubert, Julia Buitink, Jerome Gouzy, Jean-Marie Prosperie, Judith Burstin, Richard Thompson, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Diversité et adaptation des plantes cultivées (UMR DIAPC), 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), and ProdInra, Migration

Subjects
[SDE] Environmental Sciences, seed weight, QTL, [SDV]Life Sciences [q-bio], fungi, pea, food and beverages, medicago truncatula, [SDV] Life Sciences [q-bio], endosperm, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, subtilase
Abstract

BAP Pôle GEAPSI; International audience; We have exploited the extensive synteny between the model legume Medicago truncatula and the cultivated garden pea, Pisumsativum, to identify loci controlling seed filling and seedcomposition in the crop species. QTLs for these traits are mapped by analyzing variation with in collections of recombinant inbred lines. Candidate genes with in the QTL intervals are identified by reference to the M.truncatula genomic sequence. This approach was used to uncover an endosperm subtilase that is associated with syntenic seed weight QTLs in Medicago and pea, and we discuss the possible role played by this enzyme in contributing to final seed weight.

24. Exploiting post-genomics resources in model species and genome conservation between model species and legume crops to accelerate seed biology discoveries in crops

Author

Hélène Zuber, Christine Le Signor, Gregoire Aubert, Amandine Bordat, Vincent Savois, Marion Verdenaud, Jerome Gouzy, Julia Buitink, Céline Vandecasteele, Jérôme Verdier, Udvardi, M., Jean-Claude Davidian, Markus Wirtz, Ruediger Hell, Richard Thompson, Judith Burstin, Karine Gallardo, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiologie Moléculaire des Semences (PMS), Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université Catholique de Louvain = Catholic University of Louvain (UCL), The Samuel Roberts Noble Foundation, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Heidelberg University

Subjects
GENOME CONSERVATION, GRAIN LEGUMES, SULFUR METABOLISM, LEGUME MODEL SPECIES, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, POST-GENOMIC RESOURCES, SULFUR TRANSPOR, TRANSCRIPTOME, MEDICAGO TRUNCATULA, ComputingMilieux_MISCELLANEOUS, LEGUME CROPS, PROTEOME
Abstract

International audience

25. The hidden legume roots: cluster root development in white lupin

Author

Barbara Hufnagel, André Marques, Erika Sallet, William Marande, Alexandre Soriano, Sandrine Arribat, Matthew Nelson, Fanchon Divol, Laurence MARQUES, Cecilia Gallardo, Jerome Salse, Romain Guyot, Pierre Marc Delaux, Fernando Geu-Flores, Helene Berges, Jerome Gouzy, Benjamin Peret, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Royal Botanic Gardens [Kew], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut de Recherche pour le Développement (IRD), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Royal Botanic Gardens, Kew, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (KU)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

26. Le pois, espèce modèle ?

Author

Judith Burstin, Tayeh, Nadim N., Anthony Klein, Jonathan Kreplak, Françoise Jacquin, Susete Alves Carvalho, Christelle Aluome, Sebastien Carrere, Jerome Gouzy, Corinne Cruaud, Patrick Wincker, Brunel, Dominique D., Matthieu Falque, Marie-Christine Le Paslier, Aubert, Gregoire G., Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Bayer Cropscience, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA). FRA., Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract

BAP GEAPSI; National audience; Dès avant la découverte par Gregor Mendel des lois de la génétique il y a près de 150 ans, le pois a été un modèle pour les généticiens et les physiologistes des plantes. De nombreuses mutations modifiant le développement des plantes, y compris des mutations affectant la symbiose fixatrice d’azote ont été décrites et cartographiées. De même, l’analyse des variations de caractères d’intérêt agronomique a permis de localiser de nombreuses régions chromosomiques impliquées dans les variations de ces caractères. En s’appuyant sur d’importantes ressources génétiques générées ces dernières années, nous avons notamment identifié des régions génomiques contrôlant les composantes du rendement, la qualité des graines et la tolérance à divers stress. Mais malgré son rôle historique significatif dans la découverte des lois de l’hérédité, le pois était jusqu’à récemment une espèce orpheline de la génomique. Les clés pour déchiffrer l’impressionnante diversité phénotypique présente dans cette espèce ont longtemps manqué. Sous l’impulsion des projets nationaux et internationaux ambitieux et grâce aux innovations technologiques et informatiques récentes, ces clés sont aujourd’hui disponibles. Les ressources génomiques et post-génomiques produites sont utilisées dans le cadre de différents projets (en particulier le projet d’Investissement d’Avenir PeaMUST) ayant pour objectif le développement de cette culture aux multiples atouts environnementaux et nutritionnels.

27. Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study.

Author

Emeline Deleury, Géraldine Dubreuil, Namasivayam Elangovan, Eric Wajnberg, Jean-Marc Reichhart, Benjamin Gourbal, David Duval, Olga Lucia Baron, Jérôme Gouzy, and Christine Coustau

Subjects
Medicine, Science
Abstract

Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5'-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs) of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences) belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance of gene duplication and acquisition of paralog functional diversity in the evolution of specific invertebrate immune responses.

Published
2012
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28. A gene-phenotype network based on genetic variability for drought responses reveals key physiological processes in controlled and natural environments.

Author

David Rengel, Sandrine Arribat, Pierre Maury, Marie-Laure Martin-Magniette, Thibaut Hourlier, Marion Laporte, Didier Varès, Sébastien Carrère, Philippe Grieu, Sandrine Balzergue, Jérôme Gouzy, Patrick Vincourt, and Nicolas B Langlade

Subjects
Medicine, Science
Abstract

Identifying the connections between molecular and physiological processes underlying the diversity of drought stress responses in plants is key for basic and applied science. Drought stress response involves a large number of molecular pathways and subsequent physiological processes. Therefore, it constitutes an archetypical systems biology model. We first inferred a gene-phenotype network exploiting differences in drought responses of eight sunflower (Helianthus annuus) genotypes to two drought stress scenarios. Large transcriptomic data were obtained with the sunflower Affymetrix microarray, comprising 32423 probesets, and were associated to nine morpho-physiological traits (integrated transpired water, leaf transpiration rate, osmotic potential, relative water content, leaf mass per area, carbon isotope discrimination, plant height, number of leaves and collar diameter) using sPLS regression. Overall, we could associate the expression patterns of 1263 probesets to six phenotypic traits and identify if correlations were due to treatment, genotype and/or their interaction. We also identified genes whose expression is affected at moderate and/or intense drought stress together with genes whose expression variation could explain phenotypic and drought tolerance variability among our genetic material. We then used the network model to study phenotypic changes in less tractable agronomical conditions, i.e. sunflower hybrids subjected to different watering regimes in field trials. Mapping this new dataset in the gene-phenotype network allowed us to identify genes whose expression was robustly affected by water deprivation in both controlled and field conditions. The enrichment in genes correlated to relative water content and osmotic potential provides evidence of the importance of these traits in agronomical conditions.

Published
2012
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29. Transcription reprogramming during root nodule development in Medicago truncatula.

Author

Sandra Moreau, Marion Verdenaud, Thomas Ott, Sébastien Letort, Françoise de Billy, Andreas Niebel, Jérôme Gouzy, Fernanda de Carvalho-Niebel, and Pascal Gamas

Subjects
Medicine, Science
Abstract

Many genes which are associated with root nodule development and activity in the model legume Medicago truncatula have been described. However information on precise stages of activation of these genes and their corresponding transcriptional regulators is often lacking. Whether these regulators are shared with other plant developmental programs also remains an open question. Here detailed microarray analyses have been used to study the transcriptome of root nodules induced by either wild type or mutant strains of Sinorhizobium meliloti. In this way we have defined eight major activation patterns in nodules and identified associated potential regulatory genes. We have shown that transcription reprogramming during consecutive stages of nodule differentiation occurs in four major phases, respectively associated with (i) early signalling events and/or bacterial infection; plant cell differentiation that is either (ii) independent or (iii) dependent on bacteroid differentiation; (iv) nitrogen fixation. Differential expression of several genes involved in cytokinin biosynthesis was observed in early symbiotic nodule zones, suggesting that cytokinin levels are actively controlled in this region. Taking advantage of databases recently developed for M. truncatula, we identified a small subset of gene expression regulators that were exclusively or predominantly expressed in nodules, whereas most other regulators were also activated under other conditions, and notably in response to abiotic or biotic stresses. We found evidence suggesting the activation of the jasmonate pathway in both wild type and mutant nodules, thus raising questions about the role of jasmonate during nodule development. Finally, quantitative RT-PCR was used to analyse the expression of a series of nodule regulator and marker genes at early symbiotic stages in roots and allowed us to distinguish several early stages of gene expression activation or repression.

Published
2011
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