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1. Combined cytogenetic and molecular methods for taxonomic verification and description of Brassica populations deriving from different origins

Author

Falentin, Cyril, primary, Hadj-Arab, Houria, additional, Aissiou, Fella, additional, Bartoli, Claudia, additional, Bazan, Giuseppe, additional, Boudet, Matéo, additional, Bousset-Vaslin, Lydia, additional, Chwikhi, Marwa, additional, Coriton, Olivier, additional, Deniot, Gwénaelle, additional, Ferreira de Carvalho, Julie, additional, Gay, Laurène, additional, Geraci, Anna, additional, Glory, Pascal, additional, Huteau, Virginie, additional, Ilahy, Riadh, additional, Ilardi, Vincenzo, additional, Jarillo, José A., additional, Meglic, Vladimir, additional, Oddo, Elisabetta, additional, Pernas, Monica, additional, Pineiro, Manuel, additional, Pipan, Barbara, additional, Rhim, Thouraya, additional, Richer, Vincent, additional, Rizza, Fulvia, additional, Ronfort, Joelle, additional, Rousseau-Gueutin, Mathieu, additional, Schicchi, Rosario, additional, Sinkovic, Lovro, additional, Taburel, Maryse, additional, Terzi, Valeria, additional, Théréné, Sylvain, additional, Tiret, Mathieu, additional, Tlili, Imen, additional, Wagner, Marie-Hélène, additional, Werner Badeck, Franz, additional, and Chèvre, Anne-Marie, additional

Published
2024
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2. Chapter The Intertwined Chloroplast and Nuclear Genome Coevolution in Plants

Author

Rousseau-Gueutin, Mathieu, Martin, Guillaume, Ferreira de Carvalho, Julie, Keller, Jean, and Aïnouche, Abdelkader

Subjects
endosymbiosis, plastome evolution, functional gene transfer, nuclear integrant of plastid DNA (nupt), nucleo-cytoplasmic interactions, bic Book Industry Communication::T Technology, engineering, agriculture::TV Agriculture & farming::TVB Agricultural science
Abstract

Photosynthetic eukaryotic cells arose more than a billion years ago through the engulfment of a cyanobacterium that was then converted into a chloroplast, enabling plants to perform photosynthesis. Since this event, chloroplast DNA has been massively transferred to the nucleus, sometimes leading to the creation of novel genes, exons, and regulatory elements. In addition to these evolutionary novelties, most cyanobacterial genes have been relocated into the nucleus, highly reducing the size, gene content, and autonomy of the chloroplast genome. In this chapter, we will first present our current knowledge on the origin and evolution of the plant plastome in the different Archaeplastida lineages (Glaucophyta, Rhodophyta, and Viridiplantae), focusing on its gene content, genome size, and structural evolution. Second, we will present the factors influencing the rate of DNA transfer from the chloroplast to the nucleus, the evolutionary fates of the nuclear integrants of plastid DNA (nupts) in their new eukaryotic environment, and the drivers of chloroplast gene functional relocation to the nucleus. Finally, we will discuss how cytonuclear interactions led to the intertwined coevolution of nuclear and chloroplast genomes and the impact of hybridization and allopolyploidy on cytonuclear interactions.

Published
2018
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5. Warnings/Cautions when collecting Brassica diversity along a large climatic gradient

Author

Falentin, Cyril, primary, Hadj-Arab, Houria, additional, Aissiou, Fella, additional, Bartoli, Claudia, additional, Bazan, Giuseppe, additional, Boudet, Mateo, additional, Bousset-Vaslin, Lydia, additional, Chwikhi, Marwa, additional, Coriton, Olivier, additional, Deniot, Gwenaelle, additional, Ferreira de Carvalho, Julie, additional, Gay, Laurene, additional, Geraci, Anna, additional, Glory, Pascal, additional, Huteau, Virginie, additional, Ilahy, Riadh, additional, Ilardi, Vicenzo, additional, Jarillo, Jose A., additional, Meglic, Vladimir, additional, Oddo, Elisabetta, additional, Pernas, Monica, additional, Manuel, Pineiro, additional, Pipan, Barbara, additional, Rhim, Thouraya, additional, Richer, Vincent, additional, Rizza, Fulvia, additional, Ronfort, Joelle, additional, Rousseau-Gueutin, Mathieu, additional, Schicchi, Rosario, additional, Sinkovic, Lovro, additional, Taburel, Maryse, additional, Terzi, Valeria, additional, Therene, Sylvain, additional, Tiret, Mathieu, additional, Tlili, Imen, additional, Werner Badeck, Franz, additional, and Chevre, Anne-Marie, additional

Published
2023
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6. Phylogenomic analysis provides insights into MADS-box and TCP gene diversification and floral development of the Asteraceae, supported by de novo genome and transcriptome sequences from dandelion (Taraxacum officinale)

Author

Xiong, Wei, primary, Risse, Judith, additional, Berke, Lidija, additional, Zhao, Tao, additional, van de Geest, Henri, additional, Oplaat, Carla, additional, Busscher, Marco, additional, Ferreira de Carvalho, Julie, additional, van der Meer, Ingrid M., additional, Verhoeven, Koen J. F., additional, Schranz, M. Eric, additional, and Vijverberg, Kitty, additional

Published
2023
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8. Transcriptome data from different floral developmental stages of sexual diploid Taraxacum officinale (common dandelion; accession FCh72, France)

Author

Xiong, Wei, Risse, Judith, Berke, Lidija, Zhao, Tao, van de Geest, Henri, Oplaat, Carla, Busscher, Marco, Ferreira de Carvalho, Julie, Van der meer, Ingrid M., Verhoeven, Koen J.F., Schranz, M.E., Vijverberg, Kitty, Xiong, Wei, Risse, Judith, Berke, Lidija, Zhao, Tao, van de Geest, Henri, Oplaat, Carla, Busscher, Marco, Ferreira de Carvalho, Julie, Van der meer, Ingrid M., Verhoeven, Koen J.F., Schranz, M.E., and Vijverberg, Kitty

Abstract

For floral expression analysis, RNAs from sexual diploid dandelion (Taraxacum officinale) accession FCh72 buds and flower heads at different developmental stages, originating from plants of cuttings of FCh72, were isolated, including young stages (0, 1 and 2) in triplicate and older stages (3 and 7) and leaves as duplicates. The samples included young, whole buds (F0S0; organs initiating, stem ~0 cm) and buds and flower heads of older stages separated through the beaks in an upper (F) and lower (S) floral part: mature buds (F1, S1; organs determined and elongated, stem ~10 cm); open flowers (F2, S2), old flowers (F3, S3; 3 days after pollination [DAP]); mature pappus (F7) and ripening seeds (S7; 7 DAP), and leaves (LF). FCh72 is a vegetative clone of a plant grown from seeds collected in May 2005 from a meadow near Chatillon, Jura, France (Lat: 46.660; Lon: 5.723; Elev. 540m; Population F3 from Verhoeven, K.J.F. and Biere, A., 2013, BMC Evol. Biol. 13: 1–8., For floral expression analysis, RNAs from sexual diploid dandelion (Taraxacum officinale) accession FCh72 buds and flower heads at different developmental stages, originating from plants of cuttings of FCh72, were isolated, including young stages (0, 1 and 2) in triplicate and older stages (3 and 7) and leaves as duplicates. The samples included young, whole buds (F0S0; organs initiating, stem ~0 cm) and buds and flower heads of older stages separated through the beaks in an upper (F) and lower (S) floral part: mature buds (F1, S1; organs determined and elongated, stem ~10 cm); open flowers (F2, S2), old flowers (F3, S3; 3 days after pollination [DAP]); mature pappus (F7) and ripening seeds (S7; 7 DAP), and leaves (LF). FCh72 is a vegetative clone of a plant grown from seeds collected in May 2005 from a meadow near Chatillon, Jura, France (Lat: 46.660; Lon: 5.723; Elev. 540m; Population F3 from Verhoeven, K.J.F. and Biere, A., 2013, BMC Evol. Biol. 13: 1–8.

Published
2023

9. Transcriptome data from a mix of flower, bud, leaf and root tissues of sexual diploid Taraxacum officinale (common dandelion; accession FCh72, France)

Author

Xiong, Wei, Risse, Judith, Berke, Lidija, Zhao, Tao, van de Geest, Henri, Oplaat, Carla, Busscher, Marco, Ferreira de Carvalho, Julie, Van der meer, Ingrid M., Verhoeven, Koen J.F., Schranz, M.E., Vijverberg, Kitty, Xiong, Wei, Risse, Judith, Berke, Lidija, Zhao, Tao, van de Geest, Henri, Oplaat, Carla, Busscher, Marco, Ferreira de Carvalho, Julie, Van der meer, Ingrid M., Verhoeven, Koen J.F., Schranz, M.E., and Vijverberg, Kitty

Abstract

This dataset was used for the gene prediction/genome annotation of the de novo genome assembly of the sexual, diploid common dandelion (Taraxacum officinale) accession FCh72. A mix of RNAs from floral, bud, leaf and root tissues was prepared. Tissues were collected from plants from cuttings of FCh72 over different days, depending on tissue availability. FCh72 is a vegetative clone of a plant grown from seeds collected in May 2005 from a meadow near Chatillon, Jura, France (Lat: 46.660; Lon: 5.723; Elev. 540m; Population F3 from Verhoeven, K.J.F. and Biere, A., 2013, BMC Evol. Biol. 13: 1–8., This dataset was used for the gene prediction/genome annotation of the de novo genome assembly of the sexual, diploid common dandelion (Taraxacum officinale) accession FCh72. A mix of RNAs from floral, bud, leaf and root tissues was prepared. Tissues were collected from plants from cuttings of FCh72 over different days, depending on tissue availability. FCh72 is a vegetative clone of a plant grown from seeds collected in May 2005 from a meadow near Chatillon, Jura, France (Lat: 46.660; Lon: 5.723; Elev. 540m; Population F3 from Verhoeven, K.J.F. and Biere, A., 2013, BMC Evol. Biol. 13: 1–8.

Published
2023

10. Phylogenomic analysis provides insights into MADS-box and TCP gene diversification and floral development of the Asteraceae, supported by de novo genome and transcriptome sequences from dandelion (Taraxacum officinale)

Author

Xiong, Wei, Risse, Judith, Berke, Lidija, Zhao, Tao, van de Geest, Henri, Oplaat, Carla, Busscher, Marco, Ferreira de Carvalho, Julie, Van der meer, Ingrid M., Verhoeven, Koen J.F., Schranz, M.E., Vijverberg, Kitty, Xiong, Wei, Risse, Judith, Berke, Lidija, Zhao, Tao, van de Geest, Henri, Oplaat, Carla, Busscher, Marco, Ferreira de Carvalho, Julie, Van der meer, Ingrid M., Verhoeven, Koen J.F., Schranz, M.E., and Vijverberg, Kitty

Abstract

The Asteraceae is the largest angiosperm family with more than 25,000 species. Individual studies have shown that MADS-box and TCP transcription factors are regulators of the development and symmetry of flowers, contributing to their iconic flower-head (capitulum) and floret. However, a systematic study of MADS-box and TCP genes across the Asteraceae is lacking. We performed a comparative analysis of genome sequences of 33 angiosperm species including our de novo assembly of diploid sexual dandelion (Taraxacum officinale) and 11 other Asteraceae to investigate the lineage-specific evolution of MADS-box and TCP genes in the Asteraceae. We compared the phylogenomic results of MADS-box and TCP genes with their expression in T. officinale floral tissues at different developmental stages to demonstrate the regulation of genes with Asteraceae-specific attributes. Here, we show that MADS-box MIKCc and TCP-CYCLOIDEA (CYC) genes have expanded in the Asteraceae. The phylogenomic analysis identified AGAMOUS-like (AG-like: SEEDSTICK [STK]-like), SEPALATA-like (SEP3-like), and TCP-PROLIFERATING CELL FACTOR (PCF)-like copies with lineage-specific genomic contexts in the Asteraceae, Cichorioideae, or dandelion. Different expression patterns of some of these gene copies suggest functional divergence. We also confirm the presence and revisit the evolutionary history of previously named “Asteraceae-Specific MADS-box genes (AS-MADS).” Specifically, we identify non-Asteraceae homologs, indicating a more ancient origin of this gene clade. Syntenic relationships support that AS-MADS is paralogous to FLOWERING LOCUS C (FLC) as demonstrated by the shared ancient duplication of FLC and SEP3.

Published
2023

13. Phylogenomic analysis provides insights into MADS-box and TCP gene diversification and floral development of the Asteraceae, supported by de novo genome and transcriptome sequences from dandelion (Taraxacum officinale).

Author

Wei Xiong, Risse, Judith, Berke, Lidija, Tao Zhao, van de Geest, Henri, Oplaat, Carla, Busscher, Marco, Ferreira de Carvalho, Julie, van der Meer, Ingrid M., Verhoeven, Koen J. F., Schranz, M. Eric, and Vijverberg, Kitty

Subjects
COMMON dandelion, DANDELIONS, GENE expression, COMPARATIVE genomics, GENETIC regulation, GENES
Abstract

The Asteraceae is the largest angiosperm family with more than 25,000 species. Individual studies have shown that MADS-box and TCP transcription factors are regulators of the development and symmetry of flowers, contributing to their iconic flower-head (capitulum) and floret. However, a systematic study of MADSbox and TCP genes across the Asteraceae is lacking. We performed a comparative analysis of genome sequences of 33 angiosperm species including our de novo assembly of diploid sexual dandelion (Taraxacum officinale) and 11 other Asteraceae to investigate the lineage-specific evolution of MADS-box and TCP genes in the Asteraceae. We compared the phylogenomic results of MADS-box and TCP genes with their expression in T. officinale floral tissues at different developmental stages to demonstrate the regulation of genes with Asteraceae-specific attributes. Here, we show that MADS-box MIKCc and TCP-CYCLOIDEA (CYC) genes have expanded in the Asteraceae. The phylogenomic analysis identified AGAMOUS-like (AG-like: SEEDSTICK [STK]-like), SEPALATA-like (SEP3-like), and TCP-PROLIFERATING CELL FACTOR (PCF)-like copies with lineage-specific genomic contexts in the Asteraceae, Cichorioideae, or dandelion. Different expression patterns of some of these gene copies suggest functional divergence. We also confirm the presence and revisit the evolutionary history of previously named "Asteraceae-Specific MADSbox genes (AS-MADS)." Specifically, we identify non-Asteraceae homologs, indicating a more ancient origin of this gene clade. Syntenic relationships support that AS-MADS is paralogous to FLOWERING LOCUS C (FLC) as demonstrated by the shared ancient duplication of FLC and SEP3. [ABSTRACT FROM AUTHOR]

Published
2023
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14. Identification and Quantification of Glucosinolates and Phenolics in a Large Panel of Brassica napus Highlight Valuable Genetic Resources for Chemical Ecology and Breeding

Author

Missinou, Anani Amegan, primary, Ferreira de Carvalho, Julie, additional, Marnet, Nathalie, additional, Delhaye, Thomas, additional, Hamzaoui, Oumayma, additional, Abdel Sayed, David, additional, Guitton, Yann, additional, Lebreton, Lionel, additional, Langrume, Christophe, additional, Laperche, Anne, additional, Delourme, Régine, additional, Manzanares-Dauleux, Maria J., additional, Bouchereau, Alain, additional, and Gravot, Antoine, additional

Published
2022
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15. Projet BrasExplor : élargir les ressources génétiques du CRB BrACySol pour Brassica oleracea et Brassica rapa

Author

FALENTIN, Cyril, RICHER, Vincent, GLORY, Pascal, DENIOT, Gwenaëlle, FERREIRA DE CARVALHO, Julie, BARTOLI-KAUTSKY, Claudia, GUILLERM-ERCKELBOUDT, Anne-Yvonne, Sylvain THÉRÉNÉ, DORÉ, Stéphane, GILET, Marie, ROUSSEAU-GUEUTIN, Mathieu, GAY, Laurène, CHÈVRE, Anne-Marie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM)

Subjects
navets, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, navettes, contraintes climatiques, Choux, contrôle génétique, diversité
Abstract

National audience; Plusieurs espèces de Brassica sont conservées au sein du Centre de Ressources Biologique BrACySol à Ploudaniel (https://www6.rennes.inrae.fr/igepp/L-IGEPP/Plateformes/BrACySol). Pour le chou (Brassica oleracea, CC,2n=18) et le navet (Brassica rapa, AA, 2n=20), les ressources comprennent essentiellement des populations fermières collectées dans les années 1980. Ces deux espèces existent cependant sous forme de populations sauvages ou férales sur l’ensemble du territoire français, et leurs collectes s’avèrent indispensables pour élargir les ressources disponibles. Dans le cadre du projet H2020 Prima BrasExplor comprenant 11 partenaires de six pays, nous proposons de collecter environ 100 populations sauvages et fermières de chacune de ces deux espèces, sur un gradient nord de la France jusqu’à la zone subsaharienne d’Afrique du Nord. Ce matériel offre une opportunité très originale (i) d’identifier les déterminants génétiques responsables de l’adaptation aux contraintes climatiques, et (ii) de valoriser des populations fermières. Nous présentons ici la méthodologie suivie, les collectes en cours sur le territoire français et les travaux qui seront engagés dans le cadre du projet BrasExplor.Ces travaux ouvrent des perspectives d’amélioration vis-à-vis des contraintes abiotiques et biotiques chez le chou, le navet, ou encore le colza (Brassica napus, AACC, 2n=38) issu de l’hybridation naturelle entre ces deux espèces diploïdes.

Published
2022
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16. Epigenomic and structural events preclude recombination in Brassica napus

Author

Boideau, Franz, primary, Richard, Gautier, additional, Coriton, Olivier, additional, Huteau, Virginie, additional, Belser, Caroline, additional, Deniot, Gwenaelle, additional, Eber, Frédérique, additional, Falentin, Cyril, additional, Ferreira de Carvalho, Julie, additional, Gilet, Marie, additional, Lodé‐Taburel, Maryse, additional, Maillet, Loeiz, additional, Morice, Jérôme, additional, Trotoux, Gwenn, additional, Aury, Jean‐Marc, additional, Chèvre, Anne‐Marie, additional, and Rousseau‐Gueutin, Mathieu, additional

Published
2022
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17. Long-read assembly of the Brassica napus reference genome Darmor-bzh

Author

Rousseau-Gueutin, Mathieu, Belser, Caroline, Da silva, Corinne, Richard, Gautier, Istace, Benjamin, Cruaud, Corinne, Falentin, Cyril, Boideau, Franz, Boutte, Julien, Delourme, Régine, Deniot, Gwenaëlle, Engelen, Stefan, Ferreira de Carvalho, Julie, Lemainque, Arnaud, Maillet, Loeiz, Morice, Jérôme, Wincker, Patrick, Denoeud, France, Chèvre, Anne-Marie, Aury, Jean-Marc, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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), 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), 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), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Genoscope, the Commissariat à l'Energie Atomique et aux Énergies Alternatives, China Earthquake Administration, ANR-10-INBS-09–08, France Génomique, 791 908, Horizon 2020 Framework Programme, Biology and Plant Breeding Department, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 791908,SURFinG, 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), and 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)

Subjects
assembly, Genome, oilseed rape, AcademicSubjects/SCI02254, Brassica napus, High-Throughput Nucleotide Sequencing, food and beverages, Brassica, Data Note, direct RNA, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Nanopores, chromosome-scale, optical mapping, Phenotype, nanopore sequencing, AcademicSubjects/SCI00960, Darmor-bzh
Abstract

International audience; Backgroubd: The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. Findings: Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.Conclusion: Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

Published
2020
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19. Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

Author

Boutte, Julien, primary, Maillet, Loeiz, additional, Chaussepied, Thomas, additional, Letort, Sébastien, additional, Aury, Jean-Marc, additional, Belser, Caroline, additional, Boideau, Franz, additional, Brunet, Anael, additional, Coriton, Olivier, additional, Deniot, Gwenaëlle, additional, Falentin, Cyril, additional, Huteau, Virginie, additional, Lodé-Taburel, Maryse, additional, Morice, Jérôme, additional, Trotoux, Gwenn, additional, Chèvre, Anne-Marie, additional, Rousseau-Gueutin, Mathieu, additional, and Ferreira de Carvalho, Julie, additional

Published
2020
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20. Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus

Author

Rousseau-Gueutin, Mathieu, Lucas, Jérémy, Denoeud, France, Ferreira de Carvalho, Julie, He, Zhesi, Boutte, Julien, Deniot, Gwenaëlle, Falentin, Cyril, Filangi, Olivier, Gilet, Marie-Madeleine, Legeai, Fabrice, Lodé-Taburel, Maryse, Morice, Jérôme, Trotoux, Gwenn, Aury, Jean-Marc, Barbe, Valérie, Snowdon, Rod J., Wincker, Patrick, Bancroft, Ian, Chèvre, Anne-Marie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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), University of York [York, UK], Institut für Insektenbiotechnologie [Justus-Liebig-Universität Gießen], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Rousseau-Gueutin, Mathieu, 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), and Justus-Liebig-Universität Gießen (JLU)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

21. Functional consequences of transposable elements on duplicated gene transcription and retention in polyploid Brassica species

Author

Ferreira De Carvalho, Julie, Boutte, Julien, Maillet, Loeiz, Chaussepied, Thomas, Letort, Sébastien, Deniot, Gwenaëlle, Falentin, Cyril, Gilet, Marie-Madeleine, Legeai, Fabrice, Lodé-Taburel, Maryse, Morice, Jérôme, Trotoux, Gwenn, Chèvre, Anne-Marie, Rousseau-Gueutin, Mathieu, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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 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), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-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 Bretagne-Pays de la Loire (IMT Atlantique)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

22. Co-evolution of chloroplast and nuclear genomes in flowering plants and impact of allopolyploidy on fine tune cytonuclear interactions

Author

Rousseau-Gueutin, Mathieu, Ferreira de Carvalho, Julie, Lucas, Jérémy, Deniot, Gwenaëlle, Falentin, Cyril, Archambeau, Heloïse, Gilet, Marie-Madeleine, Legeai, Fabrice, Lodé-Taburel, Maryse, Morice, Jérôme, Trotoux, Gwenn, Montes, Emilie, Aury, Jean-Marc, Barbe, Valérie, Snowdon, Rod J., He, Zhesi, Denoeud, France, Wincker, Patrick, Bancroft, Ian, Chèvre, Anne-Marie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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), Institut für Insektenbiotechnologie [Justus-Liebig-Universität Gießen], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), University of York [York, UK], 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), Justus-Liebig-Universität Gießen (JLU), and Rousseau-Gueutin, Mathieu

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

23. Identification and Quantification of Glucosinolates and Phenolics in a Large Panel of Brassica napusHighlight Valuable Genetic Resources for Chemical Ecology and Breeding

Author

Missinou, Anani Amegan, Ferreira de Carvalho, Julie, Marnet, Nathalie, Delhaye, Thomas, Hamzaoui, Oumayma, Abdel Sayed, David, Guitton, Yann, Lebreton, Lionel, Langrume, Christophe, Laperche, Anne, Delourme, Régine, Manzanares-Dauleux, Maria J., Bouchereau, Alain, and Gravot, Antoine

Abstract

Glucosinolate (GLS) and phenolic contents in Brassicaceaecontribute to biotic and abiotic stress responses. Breeding crop accessions harboring agroecologically relevant metabolic profiles require a characterization of the chemical diversity in Brassicagermplasm. This work investigates the diversity of specialized metabolites in 281 accessions of B. napus. First, an LC-HRMS2-based approach allowed the annotation of 32 phenolics and 36 GLSs, revealing 13 branched and linear alkyl-GLSs and 4 isomers of hydroxyphenylalkyl-GLSs, many of which have been rarely reported in Brassica. Then, quantitative UPLC-UV-MS-based profiling was performed in leaves and roots for the whole panel. This revealed striking variations in the content of 1-methylpropyl-GLS (glucocochlearin) and a large variation of tetra- and penta-glucosyl kaempferol derivatives among accessions. It also highlighted two main chemotypes related to sinapoyl-O-hexoside and kaempferol-O-trihexoside contents. By offering an unprecedented overview of the phytochemical diversity in B. napus, this work provides a useful resource for chemical ecology and breeding.

Published
2022
Full Text
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24. Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doubling

Author

Ferreira De Carvalho, Julie, Lucas, Jérémy, Falentin, Cyril, Deniot, Gwenaëlle, Filangi, Olivier, Gilet, Marie-Madeleine, Legeai, Fabrice, Lodé-Taburel, Maryse, Morice, Jérôme, Trotoux, Gwenn, Aury, Jean-Marc, Barbe, Valérie, Keller, Jean, Snowdon, Rod J., He, Zhesi, Denoeud, France, Wincker, Patrick, Bancroft, Ian, Chèvre, Anne-Marie, Rousseau-Gueutin, Mathieu, 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), 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), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), Justus-Liebig-Universität Gießen (JLU), University of York [York, UK], Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), and Rousseau-Gueutin, Mathieu

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

25. Shift to self-compatibility in synthetic allopolyploid Brassica napus

Author

Azibi, Thanina, Rousseau-Gueutin, Mathieu, Trotoux, Gwenn, Lodé-Taburel, Maryse, Ferreira De Carvalho, Julie, Gilet, Marie-Madeleine, Hadj-Arab, Houria, Chèvre, Anne-Marie, 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), 24105 Bab Ezzouar, Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Université des Sciences et de la Technologie Houari Boumediene = University of Sciences and Technology Houari Boumediene [Alger] (USTHB)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

26. Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill

Author

Alvarez, Mariano, Ferreira De Carvalho, Julie, Salmon, Armel, Ainouche, Malika L, Cavé-Radet, Armand, El Amrani, Abdelhak, Foster, Tammy E, Moyer, Sydney, Richards, Christina L, Ainouche, Malika, University of South Florida [Tampa] (USF), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), DEB 1419960, Division of Environmental Biology, 1556820, Division of Integrative Organismal Systems, Franco-American Fulbright Commission, 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), and 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)

Subjects
DNA, Bacterial, 0301 basic medicine, Candidate gene, Foundation species, Arabidopsis, Poaceae, Spartina alterniflora, Hydrocarbon response, Epigenesis, Genetic, Xenobiotics, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, Botany, Gene expression, Genetics, Humans, Petroleum Pollution, Epigenetics, Transcriptomics, Ecology, Evolution, Behavior and Systematics, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Volatile Organic Compounds, biology, food and beverages, 15. Life on land, biology.organism_classification, Hydrocarbons, Ecological genomics, 030104 developmental biology, chemistry, Brachypodium distachyon, Deepwater Horizon, DNA microarray, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Xenobiotic
Abstract

International audience; Despite the severe impacts of the Deepwater Horizon oil spill, the foundation plant species Spartina alterniflora proved resilient to heavy oiling, providing an opportunity to identify mechanisms of response to the anthropogenic stress of crude oil exposure. We assessed plants from oil-affected and unaffected populations using a custom DNA microarray to identify genomewide transcription patterns and gene expression networks that respond to crude oil exposure. In addition, we used T-DNA insertion lines of the model grass Brachypodium distachyon to assess the contribution of four novel candidate genes to crude oil response. Responses in S. alterniflora to hydrocarbon exposure across the transcriptome as well as xenobiotic specific response pathways had little overlap with those previously identified in the model plant Arabidopsis thaliana. Among T-DNA insertion lines of B. distachyon, we found additional support for two candidate genes, one (ATTPS21) involved in volatile production, and the other (SUVH5) involved in epigenetic regulation of gene expression, that may be important in the response to crude oil. The architecture of crude oil response in S. alterniflora is unique from that of the model species A. thaliana, suggesting that xenobiotic response may be highly variable across plant species. In addition, further investigations of regulatory networks may benefit from more information about epigenetic response pathways.

Published
2018
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27. Impact of structural variations on the meiotic stability and plant fertility of the allotetraploid B. napus (oilseed rape)

Author

Rousseau-Gueutin, Mathieu, Ferreira De Carvalho, Julie, Stoeckel, Solenn, Morice, Jérôme, Gilet, Marie-Madeleine, Eber, Frederique, Lodé-Taburel, Maryse, Trotoux, Gwenn, Falentin, Cyril, Deniot, Gwenaëlle, Huteau, Virginie, Coriton, Olivier, Pelé, Alexandre, Chèvre, Anne-Marie, Rousseau-Gueutin, Mathieu, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

28. How a polyploid becomes a new species: example from the Brassica model

Author

Rousseau-Gueutin, Mathieu, Ferreira De Carvalho, Julie, Lucas, J., Denoued, F., Legeai, Fabrice, He, Z., Morice, Jérôme, Lodé-Taburel, Maryse, Boutte, Julien, Deniot, Gwenaëlle, Falentin, Cyril, Filangi, Olivier, Trotoux, Gwenn, Gilet, Marie-Madeleine, Coriton, Olivier, Huteau, Virginie, Aury, J.M., Barbe, Valérie, Salse, Jérôme, Winckler, P., Snowdon, R., Bancroft, Ian, Chèvre, Anne-Marie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Rousseau-Gueutin, Mathieu, 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
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

29. Genome merger and duplication as springboards for plant invasion: Lessons from Spartina

Author

Aïnouche, Malika L., Cavé-Radet, Armand, Giraud, Delphine, Baumel, Alex, Gallego-Tévar, Blanca, Castillo, Juan, Rousseau-Gueutin, Mathieu, Boutte, Julien, Ferreira De Carvalho, Julie, Lima, Oscar, Kovarick, Alec, Leitch, Andrew R., Leitch, Ilia J., Ainouche, Abdelkhader, Cabello-Hurtado, Francisco, Amrani, Abdelhak El, Salmon, Armel, Briand, Valerie, 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 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), Universidad de Sevilla / University of Sevilla, SFEcologie, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), and Universidad de Sevilla

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

30. Structural and functional consequences of transposable elements after multiple Whole-Genome Duplication events

Author

Ferreira De Carvalho, Julie, Chaussepied, Thomas, Letort, Sébastien, Chèvre, Anne-Marie, Rousseau-Gueutin, Mathieu, 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), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), 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)-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 Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and 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)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

31. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole‐genome duplications in Brassica

Author

Ferreira de Carvalho, Julie, primary, Lucas, Jérémy, additional, Deniot, Gwenaëlle, additional, Falentin, Cyril, additional, Filangi, Olivier, additional, Gilet, Marie, additional, Legeai, Fabrice, additional, Lode, Maryse, additional, Morice, Jérôme, additional, Trotoux, Gwenn, additional, Aury, Jean‐Marc, additional, Barbe, Valérie, additional, Keller, Jean, additional, Snowdon, Rod, additional, He, Zhesi, additional, Denoeud, France, additional, Wincker, Patrick, additional, Bancroft, Ian, additional, Chèvre, Anne‐Marie, additional, and Rousseau‐Gueutin, Mathieu, additional

Published
2019
Full Text
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32. Transcriptomic responses to challenging environments in Spartina alterniflora populations

Author

Richards, Christina L., Alvarez, Mariano, Ferreira De Carvalho, Julie, Cavé-Radet, Armand, Amrani, Abdelhak El, Foster, Tammy E., Moyer, Sydney, Salmon, Armel, Aïnouche, Malika L., Department of Integrative Biology, University of South Florida [Tampa] (USF), 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), Briand, Valerie, 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), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

34. The relative roles of local climate adaptation and phylogeny in determining leaf-out timing of temperate tree species

Author

Desnoues, Elsa, Ferreira de Carvalho, Julie, Zohner, Constantin M., Crowther, Thomas W., Desnoues, Elsa, Ferreira de Carvalho, Julie, Zohner, Constantin M., and Crowther, Thomas W.

Abstract

Leaf out times of temperate forest trees are a prominent determinant of global carbon dynamics throughout the year. Abiotic cues of leaf emergence are well studied but investigation of the relative roles of shared evolutionary history (phylogeny) and local adaptation to climate in determining the species-level responses to these cues is needed to better apprehend the effect of global change on leaf emergence. We explored the relative importance of phylogeny and climate in determining the innate leaf out phenology across the temperate biome.

Published
2017

35. Genome merger as evolutionary springboard: Insights from recurrent hybridization and polyploidy in Spartina

Author

Aïnouche, Malika L., Chelaifa, Houda, Rousseau-Gueutin, Mathieu, Boutte, Julien, Rousseau, Hélène, Ferreira De Carvalho, Julie, Amrani, Abdelhak El, Cavé-Radet, Armand, Kovarik, Ales, Leitch, Ilia J, Leitch, Andrew, Ainouche, Abdelkhader, Salmon, Armel, 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), Sch Biol & Chem Sci, Queen Mary University of London (QMUL), Briand, Valerie, 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), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

36. Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion

Author

Verhoeven, Koen J. F., primary, Verbon, Eline H., additional, van Gurp, Thomas P., additional, Oplaat, Carla, additional, Ferreira de Carvalho, Julie, additional, Morse, Alison M., additional, Stahl, Mark, additional, Macel, Mirka, additional, and McIntyre, Lauren M., additional

Published
2017
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38. Polyploidy, genome evolution and functional novelty in genus SpartinaI (Poaceae)

Author

Ainouche, Malika, Rousseau-Gueutin, Mathieu, Rousseau, Hélène, Boutte, Julien, Bellot, Sidonie, Ferreira de Carvalho, Julie, Salmon, Armel, 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), 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), and Briand, Valerie

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

39. The challenges of genomics in polyploidy Spartina species: How to deal with hybrid genomes and high redundancy?

Author

Salmon, Armel, Boutte, Julien, Ferreira de Carvalho, Julie, Rousseau-Gueutin, Mathieu, Aïnouche, Malika L., Briand, Valerie, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), 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), and 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)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

40. Impact of whole genome triplication on the evolutionary history and the functional dynamics of regulatory genes involved in Brassicaself-incompatibility signalling pathway

Author

Azibi, Thanina, Hadj-Arab, Houria, Lodé, Maryse, Ferreira de Carvalho, Julie, Trotoux, Gwenn, Nègre, Sylvie, Gilet, Marie-Madeleine, Boutte, Julien, Lucas, Jérémy, Vekemans, Xavier, Chèvre, Anne-Marie, and Rousseau-Gueutin, Mathieu

Abstract

Polyploidy or whole genome duplication is a frequent and recurrent phenomenon in flowering plants that has played a major role in their diversification, adaptation and speciation. The adaptive success of polyploids relates to the different evolutionary fates of duplicated genes. In this study, we explored the impact of the whole genome triplication (WGT) event in the Brassiceae tribe on the genes involved in the self-incompatibility (SI) signalling pathway, a mechanism allowing recognition and rejection of self-pollen in hermaphrodite plants. By taking advantage of the knowledge acquired on this pathway as well as of several reference genomes in Brassicaceae species, we determined copy number of the different genes involved in this pathway and investigated their structural and functional evolutionary dynamics. We could infer that whereas most genes involved in the SI signalling returned to single copies after the WGT event (i.e. ARC1, JDP1, THL1, THL2, Exo70A01) in diploid Brassicaspecies, a few were retained in duplicated (GLO1and PLDα) or triplicated copies (MLPK). We also carefully studied the gene structure of these latter duplicated genes (including the conservation of functional domains and active sites) and tested their transcription in the stigma to identify which copies seem to be involved in the SI signalling pathway. By taking advantage of these analyses, we then explored the putative origin of a contrasted SI phenotype between two Brassica rapavarieties that have been fully sequenced and shared the same S-allele (S60).

Published
2020
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41. Heritable gene expression differences between apomictic clone members in Taraxacum officinale : Insights into early stages of evolutionary divergence in asexual plants

Author

Ferreira de Carvalho, Julie, Oplaat, Carla, Pappas, Nikolaos, Derks, Martijn, de Ridder, Dick, Verhoeven, Koen J.F., Ferreira de Carvalho, Julie, Oplaat, Carla, Pappas, Nikolaos, Derks, Martijn, de Ridder, Dick, and Verhoeven, Koen J.F.

Abstract

Background: Asexual reproduction has the potential to enhance deleterious mutation accumulation and to constrain adaptive evolution. One source of mutations that can be especially relevant in recent asexuals is activity of transposable elements (TEs), which may have experienced selection for high transposition rates in sexual ancestor populations. Predictions of genomic divergence under asexual reproduction therefore likely include a large contribution of transposable elements but limited adaptive divergence. For plants empirical insight into genome divergence under asexual reproduction remains limited. Here, we characterize expression divergence between clone members of a single apomictic lineage of the common dandelion (Taraxacum officinale) to contribute to our knowledge of genome evolution under asexuality. Results: Using RNA-Seq, we show that about one third of heritable divergence within the apomictic lineage is driven by TEs and TE-related gene activity. In addition, we identify non-random transcriptional differences in pathways related to acyl-lipid and abscisic acid metabolisms which might reflect functional divergence within the apomictic lineage. We analyze SNPs in the transcriptome to assess genetic divergence between the apomictic clone members and reveal that heritable expression differences between the accessions are not explained simply by genome-wide genetic divergence. Conclusion: The present study depicts a first effort towards a more complete understanding of apomictic plant genome evolution. We identify abundant TE activity and ecologically relevant functional genes and pathways affecting heritable within-lineage expression divergence. These findings offer valuable resources for future work looking at epigenetic silencing and Cis-regulation of gene expression with particular emphasis on the effects of TE activity on asexual species' genome.

Published
2016

43. Hybridation, polyploidie et evolution des génomes : le cas des spartines envahissant les marais salés

Author

Ainouche, Malika, Salmon, Armel, Rousseau-Gueutin, Mathieu, Boutte, Julien, Rousseau, Hélène, Ferreira De Carvalho, Julie, Bellot, Sidonie, Chelaifa, Houda, Fortune, Philippe, Baumel, Alex, Aïnouche, Abdelkader, Misset, Marie-Thérèse, 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), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), 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), UMR CNRS 6553 ECOBIO, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), and Briand, Valerie

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

44. Transcriptomic response to hydrocarbon stress in Spartina alterniflora

Author

Alvarez, Mariano, Salmon, Armel, Ferreira De Carvalho, Julie, Ainouche, Malika, Richards, Christina L., Department of Integrative Biology, University of South Florida [Tampa] (USF), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), UMR CNRS 6553 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), and Briand, Valerie

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

45. The challenges of genomics in polyploid Spartina species: How to deal with hydrid genomes and high redundancy?

Author

Salmon, Armel, Boutte, Julien, Ferreira de Carvalho, Julie, Rousseau-Gueutin, Mathieu, Ainouche, Malika, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), 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), and Briand, Valerie

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

46. Recurrent polyploidy in the salt marsh Genus spartina: lessons and challenges : [W630]

Author

Ainouche, Malika Lily, Ferreira de Carvalho, Julie, Boutte, Julien, Bellot, Sidonie, Rousseau-Gueutin, Mathieu, Ainouche, Abdelkader, Charron, Carine, D'Hont, Angélique, Leitch, Andrew, Kovarik, Ales, and Salmon, Armel

Subjects
F30 - Génétique et amélioration des plantes
Abstract

Genus Spartina (Poaceae, Chloridoideae) is characterized by recurrent hybridization and genome duplication. Species introduction outside their native range had dramatic ecological and evolutionary consequences. This genus contains a notorious example of neopolyploidy, namely the invasive allododecaploid species Spartina anglica. This species formed in southern England during the 19 century, following genome duplication of the sterile F1 hybrid S. x townsendii which resulted from hybridization between two hexaploid species, the introduced Spartina alterniflora and the native Spartina maritima. Spartina anglica has larger ecological amplitude than its parents and has rapidly colonized the European saltmarshes and it is now introduced in several continents. Another sterile F1 hybrid (S. x neyrautii) was also formed independently from the same parents in South-West France. This system allows examining the consequences of polyploidy at various evolutionary time scales, and most particularly the consequences of recent polyploid speciation in natural populations in a well-understood historical and phylogenetic framework. It also allows distinguishing the effects of two important components of allopolyploid speciation: interspecific hybridization (in S. x townsendii and S. x neyrautii) and genome duplication (in S. anglica). We have employed various molecular approaches to decipher the evolutionary history of the genus, the genomic and transcriptomic effects of allopolyploidy. As Spartina belongs to one of the poorest investigated lineage in the Poaceae family from the genomic perspective, we have developed various genomic resources (massive parallel sequencing, reference transcriptomes, BAC sequencing) which are now employed for the challenging analysis of the evolution of such highly redundant genomes. (Texte intégral)

Published
2014

50. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

Author

Boutte, Julien, primary, Aliaga, Benoît, additional, Lima, Oscar, additional, Ferreira de Carvalho, Julie, additional, Ainouche, Abdelkader, additional, Macas, Jiri, additional, Rousseau-Gueutin, Mathieu, additional, Coriton, Olivier, additional, Ainouche, Malika, additional, and Salmon, Armel, additional

Published
2016
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