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2. A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae

Author

Raimondeau, Pauline, primary, Ksouda, Sayam, additional, Marande, William, additional, Fuchs, Anne-Laure, additional, Gryta, Hervé, additional, Theron, Anthony, additional, Puyoou, Aurore, additional, Dupin, Julia, additional, Cheptou, Pierre-Olivier, additional, Vautrin, Sonia, additional, Valière, Sophie, additional, Manzi, Sophie, additional, Baali-Cherif, Djamel, additional, Chave, Jérôme, additional, Christin, Pascal-Antoine, additional, and Besnard, Guillaume, additional

Published
2024
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3. Characterization of the RNA Mycovirome Associated with Grapevine Fungal Pathogens: Analysis of Mycovirus Distribution and Their Genetic Variability within a Collection of Botryosphaeriaceae Isolates

Author

Comont, Gwenaëlle, primary, Faure, Chantal, additional, Candresse, Thierry, additional, Laurens, Marie, additional, Valière, Sophie, additional, Lluch, Jérôme, additional, Lefebvre, Marie, additional, Gambier, Sébastien, additional, Jolivet, Jérôme, additional, Corio-Costet, Marie-France, additional, and Marais, Armelle, additional

Published
2024
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5. Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles.

Author

Devailly, Guillaume, Fève, Katia, Saci, Safia, Sarry, Julien, Valière, Sophie, Lluch, Jérôme, Bouchez, Olivier, Ravon, Laure, Billon, Yvon, Gilbert, Hélène, Riquet, Juliette, Beaumont, Martin, and Demars, Julie

Subjects
DNA methylation, DUODENUM, SWINE farms, TRANSCRIPTOMES, SWINE, TIGHT junctions
Abstract

Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low-(LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite

Author

Sallé, Guillaume, primary, Courtot, Elise, additional, Cabau, Cédric, additional, Parrinello, Hugues, additional, Serreau, Delphine, additional, Reigner, Fabrice, additional, Gesbert, Amandine, additional, Jacquinot, Lauriane, additional, Lenhof, Océane, additional, Aimé, Annabelle, additional, Picandet, Valérie, additional, Kuzmina, Tetiana, additional, Holovachov, Oleksandr, additional, Bellaw, Jennifer, additional, Nielsen, Martin K, additional, von Samson-Himmelstjerna, Georg, additional, Valière, Sophie, additional, Gislard, Marie, additional, Lluch, Jérôme, additional, Kuchly, Claire, additional, and Klopp, Christophe, additional

Published
2023
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9. A Selective Bottleneck During Host Entry Drives the Evolution of New Legume Symbionts

Author

Doin de Moura, Ginaini Grazielli, primary, Mouffok, Saida, additional, Gaudu, Nil, additional, Cazalé, Anne-Claire, additional, Milhes, Marine, additional, Bulach, Tabatha, additional, Valière, Sophie, additional, Roche, David, additional, Ferdy, Jean-Baptiste, additional, Masson-Boivin, Catherine, additional, Capela, Delphine, additional, and Remigi, Philippe, additional

Published
2023
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10. A dual legume‐rhizobium transcriptome of symbiotic nodule senescence reveals coordinated plant and bacterial responses

Author

Sauviac, Laurent, primary, Rémy, Antoine, additional, Huault, Emeline, additional, Dalmasso, Mélanie, additional, Kazmierczak, Théophile, additional, Jardinaud, Marie‐Françoise, additional, Legrand, Ludovic, additional, Moreau, Corentin, additional, Ruiz, Bryan, additional, Cazalé, Anne‐Claire, additional, Valière, Sophie, additional, Gourion, Benjamin, additional, Dupont, Laurence, additional, Gruber, Véronique, additional, Boncompagni, Eric, additional, Meilhoc, Eliane, additional, Frendo, Pierre, additional, Frugier, Florian, additional, and Bruand, Claude, additional

Published
2022
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12. Transcriptomic and DNA methylation response to feed intake in the duodenum in high- and low- feed efficiency pig lines

Author

Devailly, Guillaume, Fêve, Katia, Saci, Safia, Sarry, Julien, Valière, Sophie, Bouchez, Olivier, Ravon, Laure, Billon, Yvon, Beaumont, Martin, Gilbert, Hélène, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Expérimentale Elevages Porcins Innovants (GenESI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French Minister of Higher Education, Research and Innovation (APAFIS#21107-2018120415595562 v10), and Devailly, Guillaume

Subjects
[SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Abstract

International audience; Feed efficiency is a complex trait of interest in animal breeding to reduce environmental impact of livestock herding and the cost of animal feed. A divergent selection on feed efficiency was carried out in pigs for more than 10 generations at an INRAE experimental unit, establishing lines of relative high- and low-feed efficiency in large white pigs. The objective of this study was to identify the molecular mechanisms underlying the divergence in feed efficiency between the two pig lines in the duodenum. We focused on the duodenum because of its sensory role in the hunger satiety pathways.Duodenum mucosal samples were collected in post-weaning pigs from the two divergent lines either after a 12 h period of feed restriction, or with a 10 h period of feed restriction followed by a 2 h period of ad libitum feed access (n = 6 per group and per line). Transcritomes and methylomes were analysed by poly-A RNA sequencing (RNA-seq) and by methylated DNA precipitation followed by sequencing (MeDP-seq), respectively. Transcriptomic reads were analysed with nf-core/rnaseq and limma-voom. MeDP-seq reads were analysed with nf-core/chipseq and the BayMeth method.A total of 962 genes were differentially expressed in the duodenum mucosa between the conditions (fasted vs fed), in contrast with 318 differentially expressed genes when comparing the divergent lines. The DNA methylome of the duodenum mucosa was unaffected by short term feed intake, but was distinct between the lines. More transcripts were affected by short term feed intake in the feed-efficient line than in the other line, including genes of the incretine secretion pathways involved in the production of GIP and GLP-1.Thus the duodenum transcriptomic response to short term feed intake was distinct in feed efficient and less efficient pig lines. These differences might in part be due to differences in DNA methylation profiles.

Published
2022
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13. A Selective Bottleneck During Host Entry Drives the Evolution of New Legume Symbionts.

Author

Moura, Ginaini Grazielli Doin de, Mouffok, Saida, Gaudu, Nil, Cazalé, Anne-Claire, Milhes, Marine, Bulach, Tabatha, Valière, Sophie, Roche, David, Ferdy, Jean-Baptiste, Masson-Boivin, Catherine, Capela, Delphine, and Remigi, Philippe

Subjects
PHYTOPATHOGENIC bacteria, PLANT life cycles, ROOT-tubercles, LIFE cycles (Biology), BACTERIAL adaptation, PHENOTYPIC plasticity, SYMBIODINIUM, RHIZOBIUM
Abstract

During the emergence of new host–microbe symbioses, microbial fitness results from the ability to complete the different steps of symbiotic life cycles, where each step imposes specific selective pressures. However, the relative contribution of these different selective pressures to the adaptive trajectories of microbial symbionts is still poorly known. Here, we characterized the dynamics of phenotypic adaptation to a simplified symbiotic life cycle during the experimental evolution of a plant pathogenic bacterium into a legume symbiont. We observed that fast adaptation was predominantly explained by improved competitiveness for host entry, which outweighed adaptation to within-host proliferation. Whole-population sequencing of bacteria at regular time intervals along this evolution experiment revealed the continuous accumulation of new mutations (fuelled by a transient hypermutagenesis phase occurring at each cycle before host entry, a phenomenon described in previous work) and sequential sweeps of cohorts of mutations with similar temporal trajectories. The identification of adaptive mutations within the fixed mutational cohorts showed that several adaptive mutations can co-occur in the same cohort. Moreover, all adaptive mutations improved competitiveness for host entry, while only a subset of those also improved within-host proliferation. Computer simulations predict that this effect emerges from the presence of a strong selective bottleneck at host entry occurring before within-host proliferation and just after the hypermutagenesis phase in the rhizosphere. Together, these results show how selective bottlenecks can alter the relative influence of selective pressures acting during bacterial adaptation to multistep infection processes. [ABSTRACT FROM AUTHOR]

Published
2023
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14. A selective bottleneck during host entry drives the evolution of new legume symbionts

Author

Doin de Moura, Ginaini Grazielli, primary, Mouffok, Saida, additional, Gaudu, Nil, additional, Cazalé, Anne-Claire, additional, Milhes, Marine, additional, Bulach, Tabatha, additional, Valière, Sophie, additional, Roche, David, additional, Ferdy, Jean-Baptiste, additional, Masson-Boivin, Catherine, additional, Capela, Delphine, additional, and Remigi, Philippe, additional

Published
2022
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15. A la recherche de mycovirus modulant l'agressivité des Botryosphaeriaceae associés aux maladies du bois de la vigne

Author

Marais, Armelle, Faure, Chantal, Comont, Gwenaelle, Candresse, Thierry, Larignon, Philippe, Valière, Sophie, Lluch, Jerome, Bulme, Aurélien, Gambier, Sébastien, Lefebvre, Marie, Corio-Costet, M.-F., Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français de la Vigne et du Vin (IFV), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Gauthier, Muriel

Subjects
[SDV] Life Sciences [q-bio], Botryosphaeriaceae, [SDV]Life Sciences [q-bio]
Abstract

International audience

Published
2021

17. Rv0180c contributes to Mycobacterium tuberculosis cell shape and to infectivity in mice and macrophages

Author

Payros, Delphine, primary, Alonso, Henar, additional, Malaga, Wladimir, additional, Volle, Arnaud, additional, Mazères, Serge, additional, Déjean, Sébastien, additional, Valière, Sophie, additional, Moreau, Flavie, additional, Balor, Stéphanie, additional, Stella, Alexandre, additional, Combes-Soia, Lucie, additional, Burlet-Schiltz, Odile, additional, Bouchez, Olivier, additional, Nigou, Jérôme, additional, Astarie-Dequeker, Catherine, additional, and Guilhot, Christophe, additional

Published
2021
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19. Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens

Author

Feron, Romain, primary, Zahm, Margot, additional, Cabau, Cédric, additional, Klopp, Christophe, additional, Roques, Céline, additional, Bouchez, Olivier, additional, Eché, Camille, additional, Valière, Sophie, additional, Donnadieu, Cécile, additional, Haffray, Pierrick, additional, Bestin, Anastasia, additional, Morvezen, Romain, additional, Acloque, Hervé, additional, Euclide, Peter T., additional, Wen, Ming, additional, Jouano, Elodie, additional, Schartl, Manfred, additional, Postlethwait, John H., additional, Schraidt, Claire, additional, Christie, Mark R., additional, Larson, Wesley A., additional, Herpin, Amaury, additional, and Guiguen, Yann, additional

Published
2020
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20. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Author

Feron, Romain, primary, Zahm, Margot, additional, Cabau, Cédric, additional, Klopp, Christophe, additional, Roques, Céline, additional, Bouchez, Olivier, additional, Eché, Camille, additional, Valière, Sophie, additional, Donnadieu, Cécile, additional, Haffray, Pierrick, additional, Bestin, Anastasia, additional, Morvezen, Romain, additional, Acloque, Hervé, additional, Euclide, Peter T., additional, Wen, Ming, additional, Jouano, Elodie, additional, Schartl, Manfred, additional, Postlethwait, John H., additional, Schraidt, Claire, additional, Christie, Mark R., additional, Larson, Wes, additional, Herpin, Amaury, additional, and Guiguen, Yann, additional

Published
2019
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22. Estimating virus effective population size and selection without neutral markers

Author

Rousseau, Elsa, Moury, Benoît, Mailleret, Ludovic, Senoussi, Rachid, Palloix, Alain, Simon, Vincent, Valière, Sophie, Grognard, Frédéric, Fabre, Frédéric, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Biological control of artificial ecosystems (BIOCORE), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Biostatistique et Processus Spatiaux (BioSP), Génétique et Amélioration des Fruits et Légumes (GAFL), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Animalerie Rongeurs (UAR), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), SMaCH (Sustainable Management of Crop Health) metaprogramme of INRA, grant over-seen by the French National Research Agency (ANR) as part of the 'Blanc2013' program (ANR-13-BSV7- 0011, FunFit project), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Biostatistique et Processus Spatiaux (BIOSP), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), GeT PlaGe, Genotoul, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), 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), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
lcsh:Immunologic diseases. Allergy, Evolutionary Genetics, Genetic Markers, Leaves, Evolutionary Processes, Heredity, Genotype, Population Size, [SDV]Life Sciences [q-bio], Potyvirus, Variant Genotypes, Plant Science, Microbiology, Viral Evolution, Evolution, Molecular, [SPI]Engineering Sciences [physics], Population Metrics, Effective Population Size, Virology, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Genetics, Selection, Genetic, [MATH]Mathematics [math], lcsh:QH301-705.5, Plant Diseases, Evolutionary Biology, Population Biology, Models, Genetic, Plant Anatomy, Genetic Drift, Biology and Life Sciences, High-Throughput Nucleotide Sequencing, food and beverages, Organismal Evolution, Genetic Mapping, lcsh:Biology (General), Microbial Evolution, lcsh:RC581-607, Capsicum, Population Genetics, Research Article
Abstract

By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation., Author summary A growing number of experimental evolution studies are using an “evolve-and-resequence” approach to observe the within-host dynamics of pathogen variants of biomedical or ecological interest. The resulting data are particularly appropriate for studying the effects of evolutionary forces, such as selection and genetic drift, on the emergence of new pathogen variants. However, it remains challenging to unravel the effects of selection and genetic drift in the absence of neutral markers, a situation frequently encountered for microbes, such as viruses, due to their small constrained genomes. Using such an approach on a plant virus, we observed that the same set of virus variants displayed highly diverse dynamics in closely related plant genotypes. We developed and validated a method that does not require neutral markers, for estimating selection coefficients and effective population sizes from these experimental evolution data. We found that the viruses experienced considerable diversity in genetic drift regimes, depending on host genotype. Importantly, genetic drift experienced by virus populations was shown to be a heritable plant trait. These findings pave the way for the breeding of plant varieties exposing viruses to strong genetic drift, thereby slowing virus adaptation.

Published
2017
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23. Additional file 10: Figure S4. of Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

Author

Nicolas, Stéphane, Péros, Jean-Pierre, Lacombe, Thierry, Launay, Amandine, Marie-Christine Le Paslier, Bérard, Aurélie, Mangin, Brigitte, Valière, Sophie, Martins, Frédéric, Cunff, Loïc Le, Laucou, Valérie, Bacilieri, Roberto, Dereeper, Alexis, Chatelet, Philippe, This, Patrice, and Doligez, Agnès

Subjects
food and beverages
Abstract

PCA analysis of the Vassal collection and wild panel, based on SSR data. Relative position of: A. The three subgroups of the association panel. B. The genetic core collection. (PDF 254 kb)

Published
2016
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24. Additional file 6: Figure S2. of Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

Author

Nicolas, Stéphane, Péros, Jean-Pierre, Lacombe, Thierry, Launay, Amandine, Marie-Christine Le Paslier, Bérard, Aurélie, Mangin, Brigitte, Valière, Sophie, Martins, Frédéric, Cunff, Loïc Le, Laucou, Valérie, Bacilieri, Roberto, Dereeper, Alexis, Chatelet, Philippe, This, Patrice, and Doligez, Agnès

Abstract

Comparison of the distribution of the r 2 VS LD values between unlinked SNPs of the four genomic regions, corrected by both structure and one of seven kinship matrices, for the whole association panel. The boxplot for r 2 is the uncorrected reference. (PDF 76 kb)

Published
2016
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25. Additional file 9: Figure S3. of Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

Author

Nicolas, Stéphane, Péros, Jean-Pierre, Lacombe, Thierry, Launay, Amandine, Marie-Christine Le Paslier, Bérard, Aurélie, Mangin, Brigitte, Valière, Sophie, Martins, Frédéric, Cunff, Loïc Le, Laucou, Valérie, Bacilieri, Roberto, Dereeper, Alexis, Chatelet, Philippe, This, Patrice, and Doligez, Agnès

Abstract

Histogram of relatedness in the Vassal collection vs in the association panel, based on 20 SSRs. (PDF 4 kb)

Published
2016
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26. Additional file 3: Figure S1. of Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

Author

Nicolas, Stéphane, Péros, Jean-Pierre, Lacombe, Thierry, Launay, Amandine, Marie-Christine Le Paslier, Bérard, Aurélie, Mangin, Brigitte, Valière, Sophie, Martins, Frédéric, Cunff, Loïc Le, Laucou, Valérie, Bacilieri, Roberto, Dereeper, Alexis, Chatelet, Philippe, This, Patrice, and Doligez, Agnès

Subjects
mental disorders
Abstract

Position of the amplicons selected in the four LD study regions for SNP discovery by sequencing. For amplicons in red, at least one SNP was successfully genotyped with Illumina® VeraCode®. (PPTX 89 kb)

Published
2016
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29. Dynamique de la structure du microbiote des semences lors de la germination-levée

Author

Barret, Matthieu, Briand, Martial, Bonneau, Sophie, Préveaux, Anne, Valière, Sophie, Bouchez, Olivier, Simoneau, Philippe, Jacques, Marie-Agnès, Univ Angers, Okina, 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), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
[SDV] Life Sciences [q-bio], [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV]Life Sciences [q-bio], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding
Published
2015

32. Protecting the durability of major resistance genes to plant viruses with quantitative resistance

Author

Rousseau, Elsa, Fabre, Frédéric, Mailleret, Ludovic, Palloix, Alain, Simon, Vincent, Valière, Sophie, Moury, Benoît, Grognard, Frédéric, Gouzé, Jean-Luc, Biological control of artificial ecosystems (BIOCORE), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), 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), Génétique et Amélioration des Fruits et Légumes (GAFL), Département de Génétique Animale [Toulouse], Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station de Pathologie Végétale (AVI-PATHO), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Département Génétique Animale (DEPT GA), Centre National de la Recherche Scientifique (CNRS). FRA., Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM)

Subjects
quantitative resistance, [MATH.MATH-RT]Mathematics [math]/Representation Theory [math.RT], durable resistance, [SPI] Engineering Sciences [physics], [SDV]Life Sciences [q-bio], food and beverages, [MATH] Mathematics [math], [SDV] Life Sciences [q-bio], [SPI]Engineering Sciences [physics], viral evolution, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, landscape epidemiology, [INFO]Computer Science [cs], genetic drift, [MATH]Mathematics [math], [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The deployment of virus-resistant crops often leads to the emergence of resistance-breaking (RB) pathogens that suppress the yield benefit provided by the resistance (Fabre et al,2012). Although breakdowns are well known for qualitative resistances conferring total resistance to the virus, they are still poorly understood for quantitative resistances conferring partial resistance. Furthermore, it has been proved for several pathosystems that combining qualitative and quantitative resistances can increase the durability of the qualitative resistance (Palloix et al, 2009, Quenouille et al, 2013). Two mechanisms can explain this result : either (i) an increase of genetic drift in the virus population, or (ii) a decrease of the selection advantage of the RB mutant. The purpose of the ongoing work presented here is to disentangle the role of these two mechanisms on the durability of plant qualitative resistances to viruses.To investigate this, we concentrated on a pepper Potato virus Y (PVY) pathosystem on which we report consistent variability in bottlenecks undergone by viral populations at inoculation and in viral accumulation, both determined by the host genotype. We follow by high-throughput sequencing the within-host demo-genetic dynamics of several virus variants in contrasted plant genotypes, carrying a qualitative resistance and different combinations of quantitative resistances. The respective effects of genetic drift and selection are evaluated by fitting models to these data (Fabre, 2012). We further aim at predicting the potential of combining qualitative and quantitative plant resistances to achieve sustainable plant resistance management at the epidemic scale.

Published
2014

33. High-throughput sequencing of kDNA amplicons for the analysis of <italic>Leishmania</italic> minicircles and identification of Neotropical species.

Author

Morand, Serge, KOCHER, ARTHUR, VALIÈRE, SOPHIE, BAÑULS, ANNE-LAURE, and MURIENNE, JÉRÔME

Subjects
NUCLEOTIDE sequencing, KINETOPLASTS, LEISHMANIA, POLYMERASE chain reaction, DNA primers
Abstract

SUMMARY: Leishmania kinetoplast DNA contains thousands of small circular molecules referred to as kinetoplast DNA (kDNA) minicercles. kDNA minicircles are the preferred targets for sensitive Leishmania detection, because they are present in high copy number and contain conserved sequence blocks in which polymerase chain reaction (PCR) primers can be designed. On the other hand, the heterogenic nature of minicircle networks has hampered the use of this peculiar genomic region for strain typing. The characterization of Leishmania minicirculomes used to require isolation and cloning steps prior to sequencing. Here, we show that high-throughput sequencing of single minicircle PCR products allows bypassing these laborious laboratory tasks. The 120 bp long minicircle conserved region was amplified by PCR from 18 Leishmania strains representative of the major species complexes found in the Neotropics. High-throughput sequencing of PCR products enabled recovering significant numbers of distinct minicircle sequences from each strain, reflecting minicircle class diversity. Minicircle sequence analysis revealed patterns that are congruent with current hypothesis of Leishmania relationships. Then, we show that a barcoding-like approach based on minicircle sequence comparisons may allow reliable identifications of Leishmania spp. This work opens up promising perspectives for the study of kDNA minicercles and a variety of applications in Leishmania research. [ABSTRACT FROM AUTHOR]

Published
2018
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34. Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

Author

Nicolas, Stéphane D., primary, Péros, Jean-Pierre, additional, Lacombe, Thierry, additional, Launay, Amandine, additional, Le Paslier, Marie-Christine, additional, Bérard, Aurélie, additional, Mangin, Brigitte, additional, Valière, Sophie, additional, Martins, Frédéric, additional, Le Cunff, Loïc, additional, Laucou, Valérie, additional, Bacilieri, Roberto, additional, Dereeper, Alexis, additional, Chatelet, Philippe, additional, This, Patrice, additional, and Doligez, Agnès, additional

Published
2016
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35. The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline

Author

Lluch, Jérôme, primary, Servant, Florence, additional, Païssé, Sandrine, additional, Valle, Carine, additional, Valière, Sophie, additional, Kuchly, Claire, additional, Vilchez, Gaëlle, additional, Donnadieu, Cécile, additional, Courtney, Michael, additional, Burcelin, Rémy, additional, Amar, Jacques, additional, Bouchez, Olivier, additional, and Lelouvier, Benjamin, additional

Published
2015
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36. Emergence Shapes the Structure of the Seed Microbiota

Author

Barret, Matthieu, primary, Briand, Martial, additional, Bonneau, Sophie, additional, Préveaux, Anne, additional, Valière, Sophie, additional, Bouchez, Olivier, additional, Hunault, Gilles, additional, Simoneau, Philippe, additional, and Jacques, Marie-Agnès, additional

Published
2015
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37. Complete genome sequence of a field strain of peste des petits ruminants virus Iisolated during 2010-2014 epidemics in Senegal

Author

Salami, Habib, Croville, Guillaume, Kwiatek, Olivier, Mariette, Jérôme, Klopp, Christophe, Valière, Sophie, Guerin, Jean-Luc, Lo, Moustapha, Thiongane, Yaya, Albina, Emmanuel, Libeau, Geneviève, Salami, Habib, Croville, Guillaume, Kwiatek, Olivier, Mariette, Jérôme, Klopp, Christophe, Valière, Sophie, Guerin, Jean-Luc, Lo, Moustapha, Thiongane, Yaya, Albina, Emmanuel, and Libeau, Geneviève

Abstract

Peste des petits ruminants virus (PPRV) infection is expanding and results in regular epizootic activities in Africa, the Middle East, and Asia. Here, we report the complete genome sequence of a field strain of PPRV isolated in Senegal (SnDk11I13) in 2013. (Résumé d'auteur)

Published
2014

38. Complete Genome Sequence of a Field Strain of Peste des Petits Ruminants Virus Isolated during 2010-2014 Epidemics in Senegal

Author

Salami, Habib, primary, Croville, Guillaume, additional, Kwiatek, Olivier, additional, Mariette, Jérôme, additional, Klopp, Christophe, additional, Valière, Sophie, additional, Guérin, Jean-Luc, additional, Lo, Moustapha, additional, Thiongane, Yaya, additional, Albina, Emmanuel, additional, and Libeau, Geneviève, additional

Published
2014
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