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1. Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei.

Author

Vinh Ha Dinh Thi, Olivier Coriton, Isabelle Le Clainche, Dominique Arnaud, Sean P Gordon, Gabriella Linc, Pilar Catalan, Robert Hasterok, John P Vogel, Joseph Jahier, and Boulos Chalhoub

Subjects
Medicine, Science
Abstract

Brachypodium hybridum (2n = 30) is a natural allopolyploid with highly divergent sub-genomes derived from two extant diploid species, B. distachyon (2n = 10) and B. stacei (2n = 20) that differ in chromosome evolution and number. We created synthetic B. hybridum allotetraploids by hybridizing various lines of B. distachyon and B. stacei. The initial amphihaploid F1 interspecific hybrids were obtained at low frequencies when B. distachyon was used as the maternal parent (0.15% or 0.245% depending on the line used) and were sterile. No hybrids were obtained from reciprocal crosses or when autotetraploids of the parental species were crossed. Colchicine treatment was used to double the genome of the F1 amphihaploid lines leading to allotetraploids. The genome-doubled F1 plants produced a few S1 (first selfed generation) seeds after self-pollination. S1 plants from one parental combination (Bd3-1×Bsta5) were fertile and gave rise to further generations whereas those of another parental combination (Bd21×ABR114) were sterile, illustrating the importance of the parental lineages crossed. The synthetic allotetraploids were stable and resembled the natural B. hybridum at the phenotypic, cytogenetic and genomic levels. The successful creation of synthetic B. hybridum offers the possibility to study changes in genome structure and regulation at the earliest stages of allopolyploid formation in comparison with the parental species and natural B. hybridum.

Published
2016
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2. Comparison of grassland plant-pollinator networks on dairy farms in three contrasting French landscapes

Author

Jérémie Goulnik, Laurent Lanore, Jean-François Odoux, Emile Delacroix, Alice Michelot-Antalik, Anne Farruggia, Isabelle Le Clainche, Patricia Faivre-Rampant, Jean-Louis Fiorelli, Sandra Novak, André Blanchetête, Jean-Noël Galliot, Marie-Christine Le Paslier, Nadia Michel, Dominique Brunel, David Genoud, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Expérimentale Systèmes d'Elevage de Ruminants de Moyenne Montagne (Herbipôle), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Etude du Polymorphisme des Génomes Végétaux (EPGV), Agro-Systèmes Territoires Ressources Mirecourt (ASTER Mirecourt), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), DGE, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Abeilles, Paysages, Interactions et Systèmes de culture (APIS)

Subjects
0106 biological sciences, Ranunculus, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Grassland, Pollinator, Centaurea jacea, Abundance (ecology), Pollen, medicine, Pollination, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, geography, geography.geographical_feature_category, biology, Ecology, Diptera, 010604 marine biology & hydrobiology, DNA bar-coding, 15. Life on land, biology.organism_classification, Hymenoptera, Agricultural practice, Habitat, Knautia arvensis, Metagenomics
Abstract

International audience; Temperate grasslands provide both habitats and flower resources for pollinators in agricultural landscapes. Plant-pollinator networks change according to local and landscape variables, which are important to identify to help conserve pollinators in grasslands. We analysed plant-pollinator networks in 18 grasslands on experimental dairy farms located in three French regions contrasting by their climate, altitude, landscape or management. We combined visual surveys and pollen DNA barcoding. Our objectives were to determine which environmental factors influence pollinator taxa abundance and diversity and differences among the visual plant-pollinator networks in the three farming regions. Flower-visiting insects were trapped in six grasslands per farm during three sessions from mid-April to mid-July along fixed 400 m2 transects. Insects were identified individually to the lowest taxonomic rank possible. Pollen carried by insects was identified using nuclear ribosomal ITS2 sequences belonging to the NCBI nucleotide database. The size and diversity of plant-pollinator networks were much larger and higher in permanent grasslands at the two farms located in lowlands (Mirecourt) and mountains (Marcenat) than those at the farm with temporary grasslands and a crop landscape (Lusignan), but the degree of specialisation (H2′) was relatively similar and low (mean of 0.46). Diptera, especially Empididae and Syrphidae, represented most plant-pollinator interactions in Mirecourt and Marcenat, while Hymenoptera were more abundant at Lusignan. The percentage of semi-natural habitats in 500 m buffers and vegetation height explained 23% of the variance in pollinator abundance. Ranunculus sp. Knautia arvensis, Centaurea jacea and Trifolium repens were key plant species in the networks. DNA metabarcoding of pollen loads identified 114 genera in addition to those identified by visual observations (+34–42 per site), reflecting insects’ floral pathways and differences in the immediate landscape among farms. This study highlighted the importance of Diptera in plant-pollinator networks and the need to conserve permanent grassland diversity to conserve pollinators.

Published
2021
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3. Thirteen New Plastid Genomes from Mixotrophic and Autotrophic Species Provide Insights into Heterotrophy Evolution in Neottieae Orchids

Author

Maria D. Logacheva, Ekaterina Zheleznaia, Michał May, Marie-Christine Le Paslier, Marc-André Selosse, Etienne Delannoy, Isabelle Le Clainche, Marcin Jakalski, Félix Lallemand, Aurélie Bérard, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institute for Information Transmission Problems, Russian Academy of Sciences [Moscow] (RAS), Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), People's Friendship University of Russia [Moscow], University of Gdańsk (UG), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Gdańsk, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Lallemand, Félix

Subjects
0106 biological sciences, Letter, DNA, Plant, [SDV]Life Sciences [q-bio], Genome, Plastid, phylogeny, 010603 evolutionary biology, 01 natural sciences, Genome, Neottieae, 03 medical and health sciences, mycoheterotrophy, Symbiosis, mixotrophy, Phylogenetics, phylogénie, Genetics, Autotroph, Plastid, mycorrhizae, Orchidaceae, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Autotrophic Processes, Phylogenetic tree, biology, food and beverages, Mycorrhiza, plastome, Heterotrophic Processes, 15. Life on land, biology.organism_classification, Biological Evolution, mixotrophie, Chloroplast DNA, Evolutionary biology
Abstract

Mixotrophic species use both organic and mineral carbon sources. Some mixotrophic plants combine photosynthesis and a nutrition called mycoheterotrophy, where carbon is obtained from fungi forming mycorrhizal symbiosis with their roots. These species can lose photosynthetic abilities and evolve full mycoheterotrophy. Besides morphological changes, the latter transition is associated with a deep alteration of the plastid genome. Photosynthesis-related genes are lost first, followed by housekeeping genes, eventually resulting in a highly reduced genome. Whether relaxation of selective constraints already occurs for the plastid genome of mixotrophic species, which remain photosynthetic, is unclear. This is partly due to the difficulty of comparing plastid genomes of autotrophic, mixotrophic, and mycoheterotrophic species in a narrow phylogenetic framework. We address this question in the orchid tribe Neottieae, where this large assortment of nutrition types occurs. We sequenced 13 new plastid genomes, including 9 mixotrophic species and covering all 6 Neottieae genera. We investigated selective pressure on plastid genes in each nutrition type and conducted a phylogenetic inference of the group. Surprisingly, photosynthesis-related genes did not experience selection relaxation in mixotrophic species compared with autotrophic relatives. Conversely, we observed evidence for selection intensification for some plastid genes. Photosynthesis is thus still under purifying selection, maybe because of its role in fruit formation and thus reproductive success. Phylogenetic analysis resolved most relationships, but short branches at the base of the tree suggest an evolutionary radiation at the beginning of Neottieae history, which, we hypothesize, may be linked to mixotrophy emergence.

Published
2019
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4. Analyse de réseaux plante-pollinisateurs pour évaluer la pollinisation des prairies dans trois zones agricoles françaises contrastées

Author

Alice Michelot, Nadia Michel, Jérémie Goulnik, Dominique Brunel, Aurélie Berard, Andre Blanchetête, Aurelie Chauveau, David GENOUD, Patricia Faivre-Rampant, Jean-Louis Fiorelli, Laurent Lanore, Isabelle Le Clainche, Sandra Novak, Jean Francois Odoux, Anne Farruggia, Laboratoire Agronomie et Environnement (LAE), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Herbipôle, DGE (DGE), Agro-Systèmes Territoires Ressources Mirecourt (ASTER Mirecourt), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Fourrages Environnement Ruminants Lusignan (FERLUS), and Abeilles, Paysages, Interactions et Systèmes de culture (APIS)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2019

5. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

Author

Jean-Marc Aury, Sébastien Duplessis, Joelle Amselem, Célia Michotey, Delphine Steinbach, Christophe Plomion, Catherine Bodénès, Valérie Barbe, Franck Salin, Jean-Charles Leplé, Patrick Wincker, Hélène Bergès, Nicolas Francillonne, Christophe Klopp, Florent Murat, Jérôme Salse, Barbara Estrada-Mairey, Isabelle Le Clainche, Antoine Kremer, Nathalie Boudet, Caroline Belser, Grégoire Le Provost, Thibault Leroy, Aurélie Canaguier, Christophe Boury, François Ehrenmann, Jonathan Mercier, Isabelle Lesur, Stéphanie Fouteau, Francis Martin, Hadi Quesneville, Cécile Guichard, Tina Alaeitabar, Christine Gaspin, Céline Lalanne, Karine Labadie, Arnaud Couloux, Corinne Da Silva, Patricia Faivre-Rampant, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)

Subjects
0301 basic medicine, genome sequence, [SDV]Life Sciences [q-bio], education, Computational biology, Genome, Quercus robur, 03 medical and health sciences, Quercus, Genetics, Gene, Ecology, Evolution, Behavior and Systematics, Phylogeny, Whole genome sequencing, Contig, biology, Models, Genetic, Molecular Sequence Annotation, Genome project, Sequence Analysis, DNA, biology.organism_classification, Fosmid, 030104 developmental biology, genomic resources, Genome, Plant, Biotechnology, Reference genome
Abstract

International audience; The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.

Published
2015
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6. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Author

Boulos, Chalhoub, France, Denoeud, Shengyi, Liu, Isobel A P, Parkin, Haibao, Tang, Xiyin, Wang, Julien, Chiquet, Harry, Belcram, Chaobo, Tong, Birgit, Samans, Margot, Corréa, Corinne, Da Silva, Jérémy, Just, Cyril, Falentin, Chu Shin, Koh, Isabelle, Le Clainche, Maria, Bernard, Pascal, Bento, Benjamin, Noel, Karine, Labadie, Adriana, Alberti, Mathieu, Charles, Dominique, Arnaud, Hui, Guo, Christian, Daviaud, Salman, Alamery, Kamel, Jabbari, Meixia, Zhao, Patrick P, Edger, Houda, Chelaifa, David, Tack, Gilles, Lassalle, Imen, Mestiri, Nicolas, Schnel, Marie-Christine, Le Paslier, Guangyi, Fan, Victor, Renault, Philippe E, Bayer, Agnieszka A, Golicz, Sahana, Manoli, Tae-Ho, Lee, Vinh Ha Dinh, Thi, Smahane, Chalabi, Qiong, Hu, Chuchuan, Fan, Reece, Tollenaere, Yunhai, Lu, Christophe, Battail, Jinxiong, Shen, Christine H D, Sidebottom, Xinfa, Wang, Aurélie, Canaguier, Aurélie, Chauveau, Aurélie, Bérard, Gwenaëlle, Deniot, Mei, Guan, Zhongsong, Liu, Fengming, Sun, Yong Pyo, Lim, Eric, Lyons, Christopher D, Town, Ian, Bancroft, Xiaowu, Wang, Jinling, Meng, Jianxin, Ma, J Chris, Pires, Graham J, King, Dominique, Brunel, Régine, Delourme, Michel, Renard, Jean-Marc, Aury, Keith L, Adams, Jacqueline, Batley, Rod J, Snowdon, Jorg, Tost, David, Edwards, Yongming, Zhou, Wei, Hua, Andrew G, Sharpe, Andrew H, Paterson, Chunyun, Guan, and Patrick, Wincker

Subjects
Evolution, Molecular, Polyploidy, Brassica napus, Chromosome Duplication, Seeds, Genome, Plant
Abstract

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Published
2014

7. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

Author

Patrick Wincker, Pascal Bento, Sahana Manoli, Agnieszka A. Golicz, G. Deniot, Shengyi Liu, Christine Sidebottom, Chu Shin Koh, Ian Bancroft, Christian Daviaud, David C. Tack, Rod J. Snowdon, Jörg Tost, Guangyi Fan, Hui Guo, Smahane Chalabi, Boulos Chalhoub, Xinfa Wang, Harry Belcram, Aurélie Chauveau, Gilles Lassalle, Jean-Marc Aury, Tae-Ho Lee, Houda Chelaifa, Jinling Meng, Christopher D. Town, Haibao Tang, Zhongsong Liu, Julien Chiquet, Andrew G. Sharpe, Salman Alamery, Chunyun Guan, Mathieu Charles, Qiong Hu, Xiyin Wang, Xiaowu Wang, Jianxin Ma, Régine Delourme, Mei Guan, Eric Lyons, Chaobo Tong, Margot Correa, Adriana Alberti, Keith L. Adams, Patrick P. Edger, Marie-Christine Le Paslier, Yunhai Lu, Corinne Da Silva, Christophe Battail, Andrew H. Paterson, Isabelle Le Clainche, Benjamin Noel, Jérémy Just, Jacqueline Batley, Jinxiong Shen, Fengming Sun, Kamel Jabbari, Karine Labadie, Michel Renard, Maria Bernard, Birgit Samans, Aurélie Canaguier, Isobel A. P. Parkin, Yong Pyo Lim, Vinh Ha Dinh Thi, Victor Renault, Meixia Zhao, David Edwards, Graham J.W. King, Nicolas Schnel, Dominique Brunel, Cyril Falentin, Reece Tollenaere, Aurélie Bérard, Yongming Zhou, Dominique Arnaud, Imen Mestiri, Philippe E. Bayer, Chuchuan Fan, Wei Hua, J. Chris Pires, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Agriculture and Agri-Food (AAFC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University (FAFU), University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Research Center for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), 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), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, National Research Council of Canada (NRC), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Genotypage, Plant Genome Mapping Laboratory, Laboratoire épigénétique et environnement, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Cologne Center for Genomics, University of Cologne, Department of Agronomy, Purdue University [West Lafayette], Department of Plant and Microbial Biology, University of California (UC), Department of Botany [Vancouver] (UBC Botany), University of British Columbia (UBC), National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), Beijing Genome Institute, Fondation Jean Dausset - Centre d’Étude du Polymorphisme Humain, College of Agronomy, Hunan Agricultural University [Changsha], Department of Horticulture, Molecular Genetics and Genomics Laboratory, Chungnam National University (CNU), School of Plant Sciences, iPlant Collaborative, University of Arizona, Department of Biology, University of York [York, UK], Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Division of Biological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Southern Cross Plant Science, Southern Cross University (SCU), School of Plant Biology, The University of Western Australia (UWA), Laboratory for Epigenetics and Environment, Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire de Mathématiques et Modélisation d'Evry, Justus-Liebig-Universität Gießen (JLU), 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), University of California, Huazhong Agricultural University, Euralis Semences, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), BIOGEMMA, Unité de Recherches Zootechniques (URZ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Limagrain, J. Craig Venter Institute, Fujian Agriculture and Forestry University, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), 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, Department of Botany, University of Missouri [Columbia], Southern Cross University, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1165 Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique ( INRA ) -Université d'Evry Val d'Essonne, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ministry of Agriculture-Chinese Academy of Agricultural Sciences ( CAAS ), Agriculture and Agri-Food [Ottawa] ( AAFC ), University of Georgia, Laboratoire de Mathématiques et Modélisation d'Evry ( LaMME ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -ENSIIE-Centre National de la Recherche Scientifique ( CNRS ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Justus Liebig University Giessen, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, National Research Council of Canada ( NRC ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), University of British Columbia ( UBC ), National Key Laboratory of Crop Genetic Improvement, Chungnam National University, Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), University of Missouri ( Saisissez le sigle en majuscules sans points ), The University of Western Australia ( UWA ), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], Brassica, rapeseed, Biology, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, chemistry.chemical_compound, Gene duplication, genetics, Epigenetics, Domestication, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], molecular evolution, Brassica napus, chromosome duplication, food and beverages, plant seed, biology.organism_classification, chemistry, Glucosinolate, Seeds, cytology, Genome, Plant, 010606 plant biology & botany
Abstract

Oilseed rape (Brassica napus L.) was formed ∼7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement., Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782

Published
2014
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8. Development of resources for comparative physical mapping between Muscadinia rotundifolia and Vitis vinifera

Author

Iritche Zah-Bi, Sophie Blanc, Marc Bras, Aurelie Canaguier, Isabelle Le Clainche, Couturat, L., Nathalie CHOISNE, Dry, I., Gouyvenoux, M., Didier Merdinoglu, Poulain, J., Hadi Quesneville, Patrick Wincker, Pere Mestre, Anne-Francoise Adam-Blondon, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)

Subjects
vitis vinifera, séquence nucleique, MUSCADINIA ROTUNDIFOLIA, GRAPEVINE, DNA SEQUENCE, [SDV]Life Sciences [q-bio], vigne, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2010

9. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance

Author

Véronique de Berardinis, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Raffaella Marconi, Sophie Paillard, Gabriele Di Gaspero, Anne-Françoise Adam-Blondon, Cécile Guichard, Isabelle Le Clainche, Legeai Fabrice, Raffaele Testolin, Véronique Brunaud, Corinne Cruaud, Michele Morgante, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Agrarie e Ambientali (DiSA), Università degli Studi di Udine - University of Udine [Italie], Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), 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, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Dipartimento di Matematica e Informatica - Universita Udine (DIMI), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut 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
0106 biological sciences, Candidate gene, carte génétique, système immunitaire, Sequence assembly, Plant Science, 01 natural sciences, Genome, Polymerase Chain Reaction, maladie fongique, lcsh:Botany, RICE GENOME, Vitis, PLANT IMMUNE SYSTEM, 2. Zero hunger, Genetics, 0303 health sciences, Vegetal Biology, Contig, NONHOST RESISTANCE, Physical Chromosome Mapping, GENOME SEQUENCE, food and beverages, ARABIDOPSIS, lcsh:QK1-989, mildiou, gène candidat, Genome, Plant, Research Article, Signal Transduction, résistance aux maladies, Heterozygote, GENETICS, Biology, Genes, Plant, DNA sequencing, Chromosomes, Plant, LINKAGE MAP, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genome size, 030304 developmental biology, Plant Diseases, BAC, Whole genome sequencing, VITIS VINIFERA L, POWDERY MILDEW, GENETIQUE, cabernet sauvignon, Sequence Analysis, DNA, séquence nucléotidique, Immunity, Innate, cartographie, vigne, Biologie végétale, 010606 plant biology & botany
Abstract

Background Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. Results The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. Conclusion Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.

Published
2008
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10. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

Author

Graziano Pesole, Benjamin Noel, François Artiguenave, Alberto Policriti, Federica Cattonaro, Alessandro Vezzi, Delphine Jublot, Valérie Laucou, Michel Gouyvenoux, Eléonore Durand, Didier Merdinoglu, Cristian Del Fabbro, Giorgio Valle, Isabelle Le Clainche, Michael Alaux, Irena Juman, Erica Mica, Béatrice Segurens, Alberto Casagrande, Claude Scarpelli, Massimo Delledonne, Gabriele Di Gaspero, Jean-Marc Aury, David S. Horner, Marco Moroldo, M. Enrico Pè, Philippe Hugueney, Mario Pezzotti, Michel Caboche, Anne-Françoise Adam-Blondon, Véronique Anthouard, Nicola Vitulo, Alain Lecharny, Alain Billault, Virginie Vico, Olivier Jaillon, Christian Clepet, Sébastien Aubourg, Michele Morgante, Jean Weissenbach, Patrick Wincker, Nathalie Choisne, Aurélie Canaguier, Corinne Dasilva, Edgardo Ugarte, Philippe Chatelet, Clémence Bruyère, Vincent Dumas, Sophie Paillard, Fabrice Legeai, Nicoletta Felice, Simone Scalabrin, G Malacrida, Julie Poulain, Francis Quetier, Claire Jubin, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Dipartimento di Matematica e Informatica - Universita Udine (DIMI), Università degli Studi di Udine - University of Udine [Italie], Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), CRIBI (CRIBI), Università degli Studi di Padova = University of Padua (Unipd), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano = University of Milan (UNIMI), Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Istituto Tecnologie Biomediche, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Dipartimento Scientifico e Tecnologico (DST), Università degli studi di Verona = University of Verona (UNIVR), Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, VIGNA-CRA Initiative (VIGNA-CRA INITIATIVE), Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Universita degli Studi di Padova, Università degli Studi di Milano [Milano] (UNIMI), Università degli studi di Bari Aldo Moro (UNIBA), Consiglio Nazionale delle Ricerche [Roma] (CNR), University of Verona (UNIVR), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Università degli studi di Milano [Milano], Università degli studi di Bari, Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Università degli Studi di Verona, O., Jaillon, J., Aury, B., Noel, A., Policriti, C., Clepet, Casagrande, Alberto, N., Choisne, S., Aubourg, N., Vitulo, C., Jubin, A., Vezzi, F., Legeai, P., Hugueney, C., Dasilva, D., Horner, E., Mica, D., Jublot, J., Poulain, C., Bruyère, A., Billault, B., Seguren, M., Gouyvenoux, E., Ugarte, F., Cattonaro, V., Anthouard, V., Vico, C., DEL FABBRO, M., Alaux, G., DI GASPERO, V., Duma, N., Felice, S., Paillard, I., Juman, M., Moroldo, S., Scalabrin, A., Canaguier, I., LE CLAINCHE, G., Malacrida, E., Durand, G., Pesole, V., Laucou, P., Chatelet, D., Merdinoglu, M., Delledonne, M., Pezzotti, A., Lecharny, C., Scarpelli, F., Artiguenave, M. E., Pè, G., Valle, M., Morgante, M., Caboche, A., ADAM BLONDON, J., Weissenbach, F., Quétier, and P., Wincker

Subjects
0106 biological sciences, genotype, Arabidopsis, POLYPLOIDY, adaptation, 01 natural sciences, Genome, RNA, Transfer, Gene duplication, plant genomics, plant genome evolution, Sequencing, Vitis, vitis vinifera, genome sequencing, 2. Zero hunger, Genetics, Plant evolution, 0303 health sciences, Multidisciplinary, food and beverages, Exons, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Paleopolyploidy, Populus, RNA, Plant, ARABIDOPSIS-THALIANA, DNA-SEQUENCE, GENE, DUPLICATION, MAP, IDENTIFICATION, EVOLUTION, DNA, Intergenic, vine, Genome, Plant, assembly, Bioinformatics, Molecular Sequence Data, Genomics, Biology, Genes, Plant, Monocotyledon, DNA sequencing, Evolution, Molecular, Polyploidy, 03 medical and health sciences, evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, angiosperm, genome, 030304 developmental biology, Whole genome sequencing, fungi, Oryza, Sequence Analysis, DNA, 15. Life on land, chronology, Introns, grapevine, MicroRNAs, polyploidy, Karyotyping, vitis classification, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract

International audience; The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

Published
2007
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11. Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome

Author

Patrick Wincker, Anne Bernole, Fabrice Legeai, Didier Merdinoglu, Sophie Paillard, Céline Vignault, Serge Delrot, Boulos Chalhoub, Marilyn Oswald, Didier Lamoureux, Michel Caboche, Isabelle Le Clainche, Anne-Françoise Adam-Blondon, Sarah Tual, Vincent Thareau, Carole Dossat, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de biotechnologie des plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)-Université Victor Segalen - Bordeaux 2-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), 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), Transport des assimilats (TA), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Génomique-Info (URGI), Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut des Sciences de la Vigne et du Vin (ISVV)-Université de Bordeaux (UB), and Clercy-Morel, Sylvie

Subjects
0106 biological sciences, Genetics, Genetic Markers, 0303 health sciences, Chromosomes, Artificial, Bacterial, In silico, UniGene, food and beverages, General Medicine, Biology, 01 natural sciences, Genome, Polymerase Chain Reaction, 03 medical and health sciences, Plant biochemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Vitis, Agronomy and Crop Science, Gene, Genome, Plant, 030304 developmental biology, 010606 plant biology & botany, Biotechnology
Abstract

International audience; Five hundred and six EST-derived markers, 313 SSR markers and 26 BAC end-derived or SCAR markers were anchored by PCR on a subset of a Cabernet Sauvignon BAC library representing six genome equivalents pooled in three dimensions. In parallel, the 12,351 EST clusters of the grapevine UniGene set (build #11) from NCBI were used to design 12,125 primers pairs and perform electronic PCR on 67,543 nonredundant BAC-end sequences. This in silico experiment yielded 1,140 positive results concerning 638 different markers, among which 602 had not been already anchored by PCR. The data obtained will provide an easier access to the regulatory sequences surrounding important genes (represented by ESTs). In total, 1,731 islands of BAC clones (set of overlapping BAC clones containing at least one common marker) were obtained and 226 of them contained at least one genetically mapped anchor. These assigned islands are very useful because they will link the genetic map and the future fingerprint-based physical map and because they allowed us to indirectly place 93 ESTs on the genetic map. The islands containing two or more mapped SSR markers were also used to assess the quality of the integrated genetic map of the grapevine genome.

Published
2006
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12. Improved full-length cDNA production based on RNA tagging by T4 DNA ligase

Author

Michel Caboche, Christian Clepet, Isabelle Le Clainche, Unité de recherche en génomique végétale (URGV), and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, DNA, Complementary, DNA Ligases, Molecular Sequence Data, Arabidopsis, Computational biology, Biology, 01 natural sciences, adn t4, 03 medical and health sciences, chemistry.chemical_compound, Rapid amplification of cDNA ends, Complementary DNA, Genetics, Genomic library, RNA, Messenger, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Cloning, Molecular, CDNA, ANALYSE FONCTIONNELLE, 5'-RACE-PCR, NAR Methods Online, 030304 developmental biology, Gene Library, chemistry.chemical_classification, 0303 health sciences, DNA ligase, Expressed sequence tag, Base Sequence, cDNA library, génome, arabidopsis thaliana, ligase, RNA, Reproducibility of Results, méthode, chemistry, RNA, Plant, Transcription Initiation Site, DNA, 010606 plant biology & botany
Abstract

Second-strand cDNA priming is a central problem for full-length characterization of transcripts. A new strategy using bacteriophage T4 DNA ligase and partially degenerate adapters is proposed for grafting a sequence tag to the end of polyribonucleotides. Based on this RNA tagging system and previously described protocols, a new method for full-length cDNA production has been implemented. Validation of the method is shown in Arabidopsis thaliana by the construction of a full-length cDNA library and the analysis of 154 clones and by 5′-RACE–PCR run on a documented experimental system.

Published
2004
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13. Molecular phylogeny of the Ceratosolen species pollinating Ficus of the subgenus Sycomorus sensu stricto: biogeographical history and origins of the species-specificity breakdown cases

Author

Carole Kerdelhué, Isabelle Le Clainche, and Jean-Yves Rasplus

Subjects
Range (biology), Population, Molecular Sequence Data, Zoology, Ficus, Biology, Models, Biological, Trees, Evolution, Molecular, Species Specificity, Phylogenetics, Genetics, Animals, Agaonidae, Rosales, education, Symbiosis, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Ceratosolen, Phylogeny, education.field_of_study, Geography, Ecology, biology.organism_classification, Cytochrome b Group, Hymenoptera, Molecular phylogenetics, Pollen, Female, Subgenus
Abstract

The 14 species of Ficus of the subgenus Sycomorus (Moraceae) are invariably pollinated by Ceratosolen species (Hym. Chalcidoidea), which in turn reproduce in the fig florets. They are distributed mostly in continental Africa, Madagascar, and the Mascarene and Comoro Islands, but 1 species extends its geographical range all over the Oriental region. Fig–pollinator relationships are usually strictly species specific, but exceptions to the ‘one-to-one’ rule occur within the group we studied. In order to understand both the biogeographical history of the Ceratosolen species associated with Ficus of the subgenus Sycomorus and the origins of the specificity breakdown cases, we have used cytochrome b sequences to reconstruct a phylogeny of the fig wasps. The results show that the pollinators from the Malagasy region and those from continental Africa form two distinct clades, which probably diverged after the crossing of the Mozambique Channel by an ancestral population. The Oriental wasp species show strong affinities with the African species. The two species-specificity exceptions are due to different evolutionary events. The occurrence of the two West African pollinators associated with F. sur can be explained by successive speciation events of the mutualistic partner without plant radiation. In contrast, we hypothesize that C. galili shifted by horizontal transfer from an unknown, presumably extinct, Ficus species to F. sycomorus after this native Malagasy fig species colonized Africa.

Published
1999

14. Molecular phylogeny of fig wasps Agaonidae are not monophyletic

Author

Carole Kerdelhué, Isabelle Le Clainche, G. Mondor, and Jean-Yves Rasplus

Subjects
0106 biological sciences, Molecular Sequence Data, Wasps, Zoology, Pollination syndrome, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Monophyly, Pollinator, RNA, Ribosomal, 28S, Animals, Agaonidae, Pteromalidae, Clade, Phylogeny, 030304 developmental biology, 0303 health sciences, Likelihood Functions, Ecology, biology, Sequence Analysis, RNA, biology.organism_classification, Molecular phylogenetics, Fig wasp
Abstract

According to the present classification, the family Agaonidae contains all fig pollinators as well as five subfamilies of non-pollinating fig wasps. The molecular phylogeny of the family was reconstructed using partial sequences of the 28S rRNA (D1 and D2 domains). Our results show that the family Agaonidae is not monophyletic. As a consequence, we restrict the famiy to the pollinator clade, and assign the non-pollinating subfamilies to various chalcid families. Sycoecinae, Otitesellinae and Sycoryctinae are included in Pteromalidae, whereas Sycophaginae and Epichrysomallinae are left unclassified and will require more in-depth morphological studies. Moreover, we proved that the fig pollination syndrome evolved only once, early in group history. The resource due to the fig-pollinator mutualism has secondarily been colonized independently by different Chalcid lineages.

Published
1998

15. Sequencing allelic BACs for exploring the level of genome heterozygosity in oak

Author

Patricia Faivre-Rampant, Nathalie Pavy, Isabelle Le Clainche, Aurelie Canaguier, Cecile Guichard, Nathalie Boudet, Philippe Leroy, Antoine Kremer, Christophe Plomion, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and ProdInra, Archive Ouverte

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, stomatognathic diseases, allelic BAC, oak, heterozygosity
Abstract

Résumé de la présentation oraleRésumé de la présentation orale; absent

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