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2. Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid

Author

Rimbault, Maud, primary, Legeai, Fabrice, additional, Peccoud, Jean, additional, Mieuzet, Lucie, additional, Call, Elsa, additional, Nouhaud, Pierre, additional, Defendini, Hélène, additional, Mahéo, Frédérique, additional, Marande, William, additional, Théron, Nicolas, additional, Tagu, Denis, additional, Le Trionnaire, Gaël, additional, Simon, Jean-Christophe, additional, and Jaquiéry, Julie, additional

Published
2023
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7. Life on the Edge: Ecological Genetics of a High Arctic Insect Species and Its Circumpolar Counterpart

Author

Simon, Jean-Christophe, Mahéo, Frédérique, Mieuzet, Lucie, Buchard, Christelle, Gauthier, Jean-Pierre, Maurice, Damien, Bonhomme, Joël, Outreman, Yannick, Hullé, Maurice, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), SILVA (SILVA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Lorraine (UL), 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), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)-AgroParisTech, and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
Artic ecosystems, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], population genetics, adaptation, colonization, A. brevicorne, Article, aphids, Acyrthosiphon svalbardicum, arctic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, geographic locations
Abstract

Arctic ecosystems are subjected to strong environmental constraints that prevent both the colonization and development of many organisms. In Svalbard, few aphid species have established permanent populations. These high arctic aphid species have developed peculiar life-history traits such as shortened life cycles and reduced dispersal capacities. Here, we present data on the distribution and population genetics of Acyrthosiphon svalbardicum in Spitsbergen, the main island of the Svalbard archipelago, and compared its genetic structure with that of its close relative Acyrthosiphon brevicorne, sampled in the top of Scandinavian mainland. We found that A. svalbardicum is common but heterogeneously distributed along the west coast of Spitsbergen. We recorded this species up to 79&deg, 12&rsquo, which constitutes the northernmost location for any aphid. Genetic structure examined using microsatellite markers showed more pronounced spatial differentiation in A. svalbardicum than in A. brevicorne populations, presumably due to reduced dispersal capacities in the former species. Although populations of A. brevicorne and A. svalbardicum were well-delineated at nuclear loci, they shared similar cytoplasmic DNA haplotypes as revealed by sequence analysis of two DNA barcodes. These results raise questions about whether these two taxa are different species, and the colonization sources and history of the Svalbard archipelago by A. svalbardicum.

Published
2019
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9. Population structure of the faba bean blight pathogen Ascochyta fabae (teleomorph, Didymella fabae) in Tunisia

Author

Ben Youssef, Noura Omri, Kerdraon, Lydie, Mieuzet, Lucie, Halila, Imen, Jammezi, Noura, Mbazia, Ahlem, Kharrat, Mohamed, Le May, Christophe, Lab Grandes Cultures, Institut National de la Recherche Agronomique de Tunisie (INRAT), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Tunis Carthage, Ministry of Agriculture, Hydraulic Resources and Fisheries, Ministry of Higher Education and Scientific Research of Tunisia, INRA (Rennes, France) [UMR IGEPP 1349], MEDILEG-ARIMNET project (2012-2015) [396], AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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
Ascochyta fabae, lcsh:Botany, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, food and beverages, population genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genetic differentiation, Ascochyta blight, faba bean, lcsh:QK1-989
Abstract

International audience; Ascochyta blight, caused by Ascochyta fabae (teleomorph: Didymella fabae) has decreased faba bean production in Tunisia and worldwide. The teleomorph has recently been observed in Tunisia, raising new questions of how to control this major disease. Isolates (317) of the pathogen were obtained between 2011 and 2013, from four geographical regions in Tunisia (Beja, Bizerte, Jendouba and Tunis). The 240 isolates obtained in 2012 were compared for mating type frequency and genetic variation by using ten polymorphic SSR markers. Of these isolates, MAT1-2 was more common (2:1) in Tunisia than MAT1-1, but this ratio can change according to population. Low to high genetic variation was detected between locations and among pathogen populations. Beja showed the greatest genotypic richness (R = 0.42), followed by Tunis (R = 0.25), Bizerte (R = 0.13), and Jendouba (R = 0.11). Indices of association (I-A) and Rd were significantly different from 0 in all the populations, suggesting high multilocus linkage disequilibrium and confirming clonal populations. Population structure of the isolates was inferred using Bayesian analyses, Principal Component Analysis (PCA), and Minimum Spanning Networks, which all revealed that the populations from each location were not distinct. Evaluating changes in seasonal genetic diversity showed low to high variances of F-ST values between the two cropping seasons in all regions. However, the PCA analysis failed to separate the A. fabae isolates sampled during the two successive seasons into two groups, indicating that these populations did not constitute distinct genetic groups. These results suggest that gene flow was limited among populations, even those separated by short geographic distances. Future studies should enlarge the number of samples of representative populations, to overcome the limitations of a small sample size and to provide a more accurate assessment of A. fabae population structure.

Published
2019
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10. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races

Author

Nouhaud, Pierre, primary, Gautier, Mathieu, additional, Gouin, Anaïs, additional, Jaquiéry, Julie, additional, Peccoud, Jean, additional, Legeai, Fabrice, additional, Mieuzet, Lucie, additional, Smadja, Carole M., additional, Lemaitre, Claire, additional, Vitalis, Renaud, additional, and Simon, Jean‐Christophe, additional

Published
2018
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11. Disentangling the Causes for Faster-X Evolution in Aphids

Author

Jaquiéry, Julie, primary, Peccoud, Jean, additional, Ouisse, Tiphaine, additional, Legeai, Fabrice, additional, Prunier-Leterme, Nathalie, additional, Gouin, Anais, additional, Nouhaud, Pierre, additional, Brisson, Jennifer A, additional, Bickel, Ryan, additional, Purandare, Swapna, additional, Poulain, Julie, additional, Battail, Christophe, additional, Lemaitre, Claire, additional, Mieuzet, Lucie, additional, Le Trionnaire, Gael, additional, Simon, Jean-Christophe, additional, and Rispe, Claude, additional

Published
2018
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12. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2013–31 May 2013

Author

Agostini, Cecilia, Albaladejo, R. G., Aparicio, A., Arthofer, Wolfgang, Berrebi, P., Boag, Peter T., Carbone, Ignazio, Conroy, Gabriel C., Cortesero, Anne-Marie, Goncalves, Evonnildo Costa, Costa, Diogo, Couto, Alvarina, De Girolamo, Mirko, Du, Hao, Fu, Shi-Jian, Garrido-Garduño, T., Gettova, L., Gilles, A., Hamoy, Igor Guerreiro, Herrera, C. M., Heussler, Carina, Isidro, Eduardo, Josso, Céline, Krapf, Patrick, Lamont, Robert W., Le Ralec, Anne, Lopes, Susana, Luis, Carla, Luo, Hui, Maheo, Frédérique, Marino, Ilaria A. M., Mieuzet, Lucie, Murray, Brent W., Ogbourne, Steven M., Pallavicini, Alberto, Parejo-Farnés, C., Patarnello, Tomaso, Paty, Chrystelle, Pereira, Carolina, Pinho, Catarina, Pinto, Pablo, Poinsot, Denis, Powell, Adrienne, Putman, Alexander I., Santoro, André, Santos, Sidney, Schlick-Steiner, Birgit C., Scott, Candace, Barbosa, Maria Silvanira, Simkova, A., Simon, Jean-Christophe, Solé-Cava, Antonio, Steiner, Florian M., Sun, Zhengxin, Torboli, Valentina, Tredway, Lane P., de Groot, Peter J. Van Coeverden, Vasconcellos, Anderson, Vázquez-Domínguez, E., Wang, Deng-Qiang, Wang, Yu-Xiang, Wei, Qi-Wei, Zane, Lorenzo, Zhang, Shu-Huan, Department of Biology, Universita degli Studi di Padova, Departamento Biología Vegetal y Ecología, Institute of Ecology, Molecular Ecology Group, University of Innsbruck, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Queen's University [Kingston], Department of Plant Pathology, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), GeneCology Research Centre, University of the Sunshine Coast, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), Instituto de Ciências Biológicas, Laboratório de Tecnologia Biomolecular, Federal University of Para - Universidade Federal do Para [Belem - Brésil], CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto [Porto], Instituto do Mar (IMAR), Department of Oceanography and Fisheries, University of the Azores, Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory of Evolutionary Physiology and Behaviour, Chongqing Key Laboratory of Animal Biology, Chongqing University, Instituto de Ecología, Departamento de Ecología de la Biodiversidad / Posgrado en Ciencias Biológicas, Universidad National Autonoma de Mexico, Faculty of Science, Department of Botany and Zoology, Masaryk University, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Universidade Federal Rural da Amazônia (UFRA), Instituto de Ciências Biológicas, Laboratório de Genética Humana e Médica, Estación Biológica de Doñana, Spanish National Research Council (CSIC), Fisheries College, Huazhong Agricultural University, Natural Resources and Environmental Studies Institute, University of Northern British Columbia (UNBC), Dipartimento di Scienze della Vita, Laboratorio di Genetica, University of Trieste, Department of Comparative Biomedicine and Food Science, Instituto de Biologia, Laboratório de Biodiversidade Molecular, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Instituto de Ciências Biológicas, Laboratório de Polimorfismo de DNA, Instituto de Ecología, Departamento de Ecología de la Biodiversidad, Università degli Studi di Padova = University of Padua (Unipd), Leopold Franzens Universität Innsbruck - University of Innsbruck, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Queen's University [Kingston, Canada], Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA), Universidade do Porto = University of Porto, Masaryk University [Brno] (MUNI), Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Huazhong Agricultural University [Wuhan] (HZAU), University of Northern British Columbia [Prince George] (UNBC), Università degli studi di Trieste = University of Trieste, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), 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), Universidade do Porto, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Cecilia, Agostini, R. G., Albaladejo, A., Aparicio, Wolfgang, Arthofer, P., Berrebi, Peter T., Boag, Ignazio, Carbone, Gabriel C., Conroy, A. M., Cortesero, Evonnildo Costa, Gonçalve, Diogo, Costa, Alvarina, Couto, MIrko De, Girolamo, Hao, Du, Shi Jian, Fu, T., Garrido Garduño, L., Gettová, A., Gille, Igor Guerreiro, Hamoy, C. M., Herrera, Carina, Heussler, Eduardo, Isidro, C., Josso, Patrick, Krapf, Robert W., Lamont, A., Le Ralec, Susana, Lope, Carla, Luí, Hui, Luo, F., Mahéo, Ilaria A. M., Marino, L., Mieuzet, Brent W., Murray, Steven M., Ogbourne, Pallavicini, Alberto, C., Parejo Farné, Tomaso, Patarnello, C., Paty, Carolina, Pereira, Catarina, Pinho, Pablo, Pinto, D., Poinsot, Adrienne, Powell, Alexander I., Putman, André, Santoro, Sidney, Santo, Birgit C., Schlick Steiner, Candace, Scott, Maria Silvanira, Barbosa, A., Šimková, J. C., Simon, Antonio Solé, Cava, Florian M., Steiner, Zhengxin, Sun, Torboli, Valentina, Lane P., Tredway, Peter J., Van Coeverden de Groot, Anderson, Vasconcello, E., Vázquez Domínguez, Deng Qiang, Wang, Yu Xiang, Wang, Qi Wei, Wei, Lorenzo, Zane, and Shu Huan, Zhang

Subjects
0106 biological sciences, 0303 health sciences, [SDV]Life Sciences [q-bio], Computational Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Databases, Genetic, micropsatellites, Genetics, Animals, Ecology, Evolution, Behavior and Systematics, Microsatellite Repeats, 030304 developmental biology, Biotechnology
Abstract

International audience; This article documents the addition of 234 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser sinensis, Aleochara bilineata, Aleochara bipustulata, Barbus meridionalis, Colossoma macropomum, Delia radicum, Drosophila nigrosparsa, Fontainea picrosperma, Helianthemum cinereum, Liomys pictus, Megabalanus azoricus, Pelteobagrus vachelli, Pleuragramma antarcticum, Podarcis hispanica type 1A, Sardinella brasiliensis and Sclerotinia homoeocarpa. These loci were cross-tested on the following species: Acipenser dabryanus, Barbus balcanicus, Barbus barbus, Barbus cyclolepis, Drosophila hydei, Drosophila melanogaster, Drosophila obscura, Drosophila subobscura, Fontainea australis, Fontainea fugax, Fontainea oraria, Fontainea rostrata, Fontainea venosa, Podarcis bocagei, Podarcis carbonelli, Podarcis liolepis, Podarcis muralis and Podarcis vaucheri.

Published
2013
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13. Genetic control of contagious asexuality in the pea aphid

Author

Jaquiéry, Julie, Peccoud, Jean, Ouisse, Tiphaine, Legeai, Fabrice, Prunier-Leterme, Nathalie, Gouin, Anaïs, Nouhaud, Pierre, Brisson, Jennifer, Bickel, Ryan, Purandare, Swapna, Poulain, Julie, Battail, Christophe, Lemaitre, Claire, Mieuzet, Lucie, Le Trionnaire, Gaël, Simon, Jean-Christophe, Rispe, Claude, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Ecologie, Evolution, Symbiose (EES), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), 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)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), University of Veterinary Medicine [Vienna] (Vetmeduni), University of Rochester [USA], Multidisciplinary Center for Advance Research and Studies (MCARS ), Jamia Milia Islamia University [New Delhi] (JMI), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), The Swiss National Science Fundation (grants PBLAA-122658 & PA00P3-139720 to JJ, http://www.snf.ch/fr/Pages/default.aspx), INRA-AIP BioRessources (project Poly-Express to DT, http://www.international.inra.fr/), The Fondation pour la Recherche pour la Biodiversité FRB (AAP-IN-2009-020 to JCS, http://www.fondationbiodiversite.fr/), The Genoscope (http://www.genoscope.cns.frspip/spip.php?lang = en), ANR-11-BSV7-0005,SPECIAPHID,Génétique de l'adaptation trophique et mécanismes d'isolement reproducteur chez les pucerons(2011), ANR-09-GENM-0017,GW-Aphid,Génomique et transcriptomique des populations pour l'identification de gènes contrôlant la variation du mode reproducteur chez le puceron du pois(2009), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), 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)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), This study was supported by the Swiss National Science Fundation (grants PBLAA-122658 & PA00P3-139720 to JJ, http://www.snf.ch/fr/Pages/default.aspx), INRA-AIP BioRessources (project Poly-Express to DT, http://www.international.inra.fr/), the Fondation pour la Recherche pour la Biodiversite´ FRB (AAP-IN-2009-020 to JCS, http://www.fondationbiodiversite.fr/), the Genoscope (http://www.genoscope.cns.frspip/spip.php?lang = en) and ANR (grant ANR-09-GENM-017-001 to DT, grant ANR-11-BSV7-005-01 to JCS and grant ANR-11-BSV7-007 to SS, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers, Université de Bretagne Sud (UBS)-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)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-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)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Male, Cancer Research, Parthenogenesis, Population genetics, Asexual reproduction, Signatures of Natural Selection, 01 natural sciences, Natural Selection, Ecological Selection, Genetics (clinical), Genetics, 0303 health sciences, education.field_of_study, Reproduction, Chromosome Mapping, Genomics, Genome Scans, Female, Anatomy, Research Article, Evolutionary Processes, lcsh:QH426-470, Gene Transfer, Horizontal, Population, Quantitative Trait Loci, Biology, 010603 evolutionary biology, Asexuality, 03 medical and health sciences, Asexual Reproduction, Reproduction, Asexual, Animals, Allele, education, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Crosses, Genetic, 030304 developmental biology, Evolutionary Biology, Obligate, Peas, Reproductive System, Biology and Life Sciences, Computational Biology, Genome Analysis, Sexual reproduction, lcsh:Genetics, Genetics, Population, Aphids, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Population Genetics
Abstract

Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of such shifts toward asexuality remain largely unknown. We addressed this issue in an aphid species where both sexual and obligate asexual lineages coexist in natural populations. These sexual and asexual lineages may occasionally interbreed because some asexual lineages maintain a residual production of males potentially able to mate with the females produced by sexual lineages. Hence, this species is an ideal model to study the genetic basis of the loss of sexual reproduction with quantitative genetic and population genomic approaches. Our analysis of the co-segregation of ∼300 molecular markers and reproductive phenotype in experimental crosses pinpointed an X-linked region controlling obligate asexuality, this state of character being recessive. A population genetic analysis (>400-marker genome scan) on wild sexual and asexual genotypes from geographically distant populations under divergent selection for reproductive strategies detected a strong signature of divergent selection in the genomic region identified by the experimental crosses. These population genetic data confirm the implication of the candidate region in the control of reproductive mode in wild populations originating from 700 km apart. Patterns of genetic differentiation along chromosomes suggest bidirectional gene flow between populations with distinct reproductive modes, supporting contagious asexuality as a prevailing route to permanent parthenogenesis in pea aphids. This genetic system provides new insights into the mechanisms of coexistence of sexual and asexual aphid lineages., Author Summary Asexual lineages occur in most groups of organisms and arise from loss of sex in sexual species. Yet, the genomic bases of these transitions remain largely unknown. Here, we combined quantitative genetic and population genomic approaches to unravel the genetic control of shifts towards permanent asexuality in the pea aphid, which conveniently shows coexisting sexual and asexual lineages. We identified one main genomic region responsible for this transition located on the X chromosome. Also, our population genetic data indicated substantial gene exchange between these reproductively distinct lineages, potentially leading to the conversion of some sexual lineages into asexual ones in a contagious manner. This genetic system provides new insights into the mechanisms of coexistence of sexual and asexual lineages.

Published
2014
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14. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races.

Author

Jaquiéry, Julie, Mieuzet, Lucie, Simon, Jean‐Christophe, Nouhaud, Pierre, Gouin, Anaïs, Legeai, Fabrice, Gautier, Mathieu, Vitalis, Renaud, Lemaitre, Claire, Peccoud, Jean, and Smadja, Carole M.

Subjects
*PEA aphid, *GENOMICS, *GENETIC polymorphisms, *CELL differentiation, *BIOLOGICAL adaptation, *PHENOTYPES
Abstract

Abstract: Identifying the genomic bases of adaptation to novel environments is a long‐term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant‐specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model‐based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population‐specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host–plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host–plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes. [ABSTRACT FROM AUTHOR]

Published
2018
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15. Are primary woody hosts 'island refuges' for host-alternating aphids and important for colonization of local cereals?

Author

Klueken, A. M., Simon, Jean-Christophe, Hondelmann, P., Mieuzet, Lucie, Gilabert, Aude, Poehling, H. -M., Hau, B., IPP ( Institute of Plant Protection ), Chinese Academy of Agricultural Sciences (CAAS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Federal Ministry of Food, Agriculture and Consumer Protection of Germany (BMELV), through the Federal Agency for Agriculture and Food (BLE) [01HS083], and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
BEAN MONOCULTURES, microsatellite genotyping, MATING SITES, L HEMIPTERA, [SDV]Life Sciences [q-bio], MICROSATELLITE MARKERS, food and beverages, PARTHENOGENETIC SITOBION APHIDS, PRUNUS-PADUS, GENETIC-STRUCTURE, Cereal aphids, density dependence, winter-to-summer host ratio, RHOPALOSIPHUM-PADI L, host alternation, ROTHAMSTED INSECT SURVEY, distance regulation, CHERRY-OAT APHID
Abstract

International audience; Only few studies are available dealing with the relation between winter host density and spatial distribution and spring colonization of winter cereals by the host-alternating cereal aphid species Rhopalosiphum padi and Metopolophium dirhodum. Large-scale studies in climatically different agroecosystems in Germany from 2004 to 2006 revealed for R.padi and M.dirhodum larger spring/summer populations in landscapes with higher densities of winter hosts. A small-scale study was performed in winter wheat fields adjacent to a large hedge with several typical winter hosts plants, bird cherry (Prunus padus) and wild rose species (Rosa spp.) to indentify distance effects (08, 824 and 2460 m). Weekly measurements of aphid density between May to July showed significantly higher densities of R.padi compared with those of other aphids. Statistical analysis (TukeyKramer test and regression analyses) revealed significant gradients from the hedge to the field centre for R.padi and M.dirhodum. In comparative studies, winged R.padi from winter and adjacent summer hosts were genotyped using four microsatellite markers. The results showed that individuals from a certain winter host were not genetically similar with individuals from neighbouring summer hosts; it, therefore, seems that winter host clones did not significantly contribute to population built-up in cereal fields over short distances. It could be concluded that on a regional scale, the density of sources for early migrants of R.padi is important for colonization intensity of surrounding summer hosts, but that the high local movement intensity and the relative small proportion of aphids that could be analysed in such tracking studies are blurring close spatial relations within short time periods.

Published
2012
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16. Admixed sexual and facultatively asexual aphid lineages at mating sites

Author

Halkett, Fabien, Plantegenest, Manuel, Prunier-Leterme, Nathalie, Mieuzet, Lucie, Delmotte, François, Simon, Jean-Christophe, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Unité 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), 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)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)

Subjects
REPRODUCTION ASEXUEE, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, GENETIQUE DES POPULATIONS, REPRODUCTION SEXUEE
Abstract

International audience; Cyclically parthenogenetic organisms may have facultative asexual counterparts. Such organisms, including aphids, are therefore interesting models for the study of ecological and genetic interactions between lineages differing in reproductive mode. Earlier studies on aphids have revealed major differences in the genetic outcomes of populations that are possibly resulting mostly either from sexual or from asexual reproduction. Besides, notable gene flow between sexual and asexual derivatives has been suspected, which could lead to the emergence of new asexual lineages. The present study examines the interplay between these lineages and is based on analyses of population structure of individuals that may contribute to the pool of sexual reproductive forms in the host alternating aphid Rhopalosiphum padi. Using a Bayesian assignment method, we first show that the sexual forms of R. padi on mating sites encompass two genetically distinct clusters of individuals in the western part of France. The first cluster included unique genotypes of sexual lineages, while the second cluster included facultatively asexual lineages in numerous copies, the reproductive mode of the two clusters being confirmed by reference clones. Sexual reproductive forms produced by sexual and facultatively asexual lineages are thus admixed at mating sites which gives a large opportunity for the two clusters to mate with each other. Nevertheless, this study also highlights, as previously demonstrated, that the two clusters retained high genetic differentiation. Possible explanations for the inferred limited genetic exchanges are advanced in the discussion, but further dedicated investigations are required to solve this paradox.

Published
2005
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18. Masculinization of the X Chromosome in the Pea Aphid

Author

Jaquiéry, Julie, primary, Rispe, Claude, additional, Roze, Denis, additional, Legeai, Fabrice, additional, Le Trionnaire, Gaël, additional, Stoeckel, Solenn, additional, Mieuzet, Lucie, additional, Da Silva, Corinne, additional, Poulain, Julie, additional, Prunier-Leterme, Nathalie, additional, Ségurens, Béatrice, additional, Tagu, Denis, additional, and Simon, Jean-Christophe, additional

Published
2013
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