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98 results on '"Berges, Helene"'

1. The Passion Fruit Genome

Author

Vieira, Maria Lucia Carneiro, Costa, Zirlane Portugal, Varani, Alessandro Mello, Sader, Mariela Analia, Cauz-Santos, Luiz Augusto, Giopatto, Helena Augusto, del Reátegui, Alina Carmen Egoávil, Bergès, Hélène, Monteiro-Vitorello, Claudia Barros, Dornelas, Marcelo Carnier, Pedrosa-Harand, Andrea, Kole, Chittaranjan, Series Editor, and Chapman, Mark A., editor

Published
2022
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3. Identifying Candidate Genes for Sugar Accumulation in Sugarcane Cultivars: From a Syntenic Genomic Region to a Gene Coexpression Network

Author

Martins, Monica Leticia Turibio, primary, Sforca, Danilo Augusto, additional, dos Santos, Luis Paulo, additional, Pimenta, Ricardo Jose Gonzaga, additional, Mancini, Melina Cristina, additional, Aono, Alexandre Hild, additional, da Silva, Claudio Benicio Cardoso, additional, Vautrin, Sonia, additional, Bellec, Arnaud, additional, Vicentini, Renato, additional, Berges, Helene, additional, da Silva, Carla Cristina, additional, and de Souza, Anete Pereira, additional

Published
2024
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4. Genetic basis and timing of a major mating system shift in Capsella

Author

Bachmann, Jörg A., Tedder, Andrew, Laenen, Benjamin, Fracassetti, Marco, Désamoré, Aurélie, Lafon-Placette, Clément, Steige, Kim A., Callot, Caroline, Marande, William, Neuffer, Barbara, Bergès, Hélène, Köhler, Claudia, Castric, Vincent, and Slotte, Tanja

Published
2019

8. FRIZZY PANICLE Drives Supernumerary Spikelets in Bread Wheat

Author

Dobrovolskaya, Oxana, Pont, Caroline, Sibout, Richard, Martinek, Petr, Badaeva, Ekaterina, Murat, Florent, Chosson, Audrey, Watanabe, Nobuyoshi, Prat, Elisa, Gautier, Nadine, Gautier, Véronique, Poncet, Charles, Orlov, Yuriy L., Krasnikov, Alexander A., Bergès, Hélène, Salina, Elena, Laikova, Lyudmila, and Salse, Jerome

Published
2015

10. Structural and functional partitioning of bread wheat chromosome 3B

Author

Choulet, Frédéric, Alberti, Adriana, Theil, Sébastien, Glover, Natasha, Barbe, Valérie, Daron, Josquin, Pingault, Lise, Sourdille, Pierre, Couloux, Arnaud, Paux, Etienne, Leroy, Philippe, Mangenot, Sophie, Guilhot, Nicolas, Le Gouis, Jacques, Balfourier, Francois, Alaux, Michael, Jamilloux, Véronique, Poulain, Julie, Durand, Céline, Bellec, Arnaud, Gaspin, Christine, Safar, Jan, Dolezel, Jaroslav, Rogers, Jane, Vandepoele, Klaas, Aury, Jean-Marc, Mayer, Klaus, Berges, Hélène, Quesneville, Hadi, Wincker, Patrick, and Feuillet, Catherine

Published
2014

15. A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

Author

Paux, Etienne, Sourdille, Pierre, Salse, Jérôme, Saintenac, Cyrille, Choulet, Frédéric, Leroy, Philippe, Korol, Abraham, Michalak, Monika, Kianian, Shahryar, Spielmeyer, Wolfgang, Lagudah, Evans, Somers, Daryl, Kilian, Andrzej, Alaux, Michael, Vautrin, Sonia, Bergès, Hélène, Eversole, Kellye, Appels, Rudi, Safar, Jan, Simkova, Hana, Dolezel, Jaroslav, Bernard, Michel, and Feuillet, Catherine

Published
2008
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16. A MITE insertion abolishes the AP3-3 self-maintenance regulatory loop in apetalous flowers of Nigella damascena.

Author

Silva, Natalia Conde e, Leguilloux, Martine, Bellec, Arnaud, Rodde, Nathalie, Aubert, Juliette, Manicacci, Domenica, Damerval, Catherine, Berges, Helene, and Deveaux, Yves

Subjects
GENE expression, MITES, GENETIC regulation, TRANSCRIPTION factors, FLOWERS, RNA splicing
Abstract

MADS-box transcription factors are important regulators of floral organ identity through their binding to specific motifs, termed CArG, in the promoter of their target genes. Petal initiation and development depend on class A and B genes, but MADS-box genes of the APETALA3 (AP3) clade are key regulators of this process. In the early diverging eudicot Nigella damascena , an apetalous [T] morph is characterized by the lack of expression of the NdAP3-3 gene, with its expression being petal-specific in the wild-type [P] morph. All [T] morph plants are homozygous for an NdAP3-3 allele with a Miniature Inverted-repeat Transposable Element (MITE) insertion in the second intron of the gene. Here, we investigated to which extent the MITE insertion impairs regulation of the NdAP3-3 gene. We found that expression of NdAP3-3 is initiated in the [T] morph, but the MITE insertion prevents its positive self-maintenance by affecting the correct splicing of the mRNA. We also found specific CArG features in the promoter of the NdAP3-3 genes with petal-specific expression. However, they are not sufficient to drive expression only in petals of transgenic Arabidopsis, highlighting the existence of Nigella -specific cis / trans -acting factors in regulating AP3 paralogs. [ABSTRACT FROM AUTHOR]

Published
2023
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19. A genome sequence resource for the genus Passiflora , the genome of the wild diploid species Passiflora organensis

Author

Costa, Zirlane Portugal, primary, Varani, Alessandro Mello, additional, Cauz‐Santos, Luiz Augusto, additional, Sader, Mariela Analía, additional, Giopatto, Helena Augusto, additional, Zirpoli, Bruna, additional, Callot, Caroline, additional, Cauet, Stephane, additional, Marande, Willian, additional, Souza Cardoso, Jessica Luana, additional, Pinheiro, Daniel Guariz, additional, Kitajima, João Paulo, additional, Dornelas, Marcelo Carnier, additional, Harand, Andrea Pedrosa, additional, Berges, Helene, additional, Monteiro‐Vitorello, Claudia Barros, additional, and Carneiro Vieira, Maria Lucia, additional

Published
2021
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20. High quality genome sequence reveals important events during domestication of White Lupin

Author

Hufnagel, B., Marques, A., Sallet, Erika, Marande, William, Soriano, A., Arribat, Sandrine, Nelson, M., Divol, F., Marques, L., Gallardo, Karine, Salse, Jerome, Guyot, R., Delaux, Pierre-Marc, Geuflores, F., Berges, Helene, Gouzy, Jerome, Péret, Benjamin, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut de Recherche pour le Développement (IRD), 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), University of Copenhagen = Københavns Universitet (UCPH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), and ProdInra, Migration

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

Prod 2019-88m BAP GEAPSI INRA; International audience; White lupin (Lupinus albus; 2n=50) is the only crop producing cluster roots, an outstanding developmental adaptation to low phosphate soils. We report a high-quality chromosome-scale assembly of white lupin genome, together with an extensive transcriptome data from ten different organs. We used singlemolecule real-time technology, in combination with short-reads sequencing and optical and genetic maps to have a successful assembly. The final assembly size is 443 Mb with a N50 of 17 Mb. About 98% of the assembled genome is included on the 25 pseudo-chromosomes. The structural annotation identified 38258 coding genes and 3,129 ncRNA, being 97.3% genes anchored on the pseudo-chromosomes. Genome of white lupin is laden with gene duplications and repetitive elements, which represent ~55% of the genome. A comparative evolutionary analysis of white lupin with other legumes revealed that it experienced a whole genome triplication in about 10 M years ago. We resequenced other 15 white lupin accessions, including a landrace and a non-domesticated variety. This has shown a highly polymorphic genome that has been impacted by domestication in different ways. Some transposons families present on the non-domesticated variety have disappeared in modern accessions, as well as the protein content of the seed has changed. Interestingly, the domestication has also modified cluster root formation. The cluster roots are formed earlier on time and closer to topsoil in the cultivated varieties. Altogether, this genome is a valuable resource and represents a keystone for legume genomics research.

Published
2019

21. Combined effects of the signal sequence and the major chaperone proteins on the export of human cytokines in Escherichia coli

Author

Berges, Helene, Joseph-Liauzun, Evelyne, and Fayet, Olivier

Subjects
Escherichia coli -- Observations, Carrier proteins -- Research, Signal peptides -- Physiological aspects, Biosynthesis -- Research, Biological transport -- Research, Biological sciences
Abstract

The formation and export of human proteins in Escherichia coli is dependent on the attached signal peptide and expression of chaperone proteins. The synthesis of the human granulocyte-macrophage colony-stimulating factor increases when it is attached to the S3 signal peptide compared to S1. The synthesis of interleukin 13 is unaffected by the signal peptide but its export into the periplasma is more if S1 is present. The overexpression of the chaperone proteins, SecB or DnaK and DnaJ, increases the concentration of the proteins in the periplasma of Escherichia coli.

Published
1996

22. The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

Author

Gautier, Mathieu, Yamaguchi, Junichi, Foucaud, Julien, Loiseau, Anne, Ausset, Aurélien, Facon, Benoit, Gschloessl, Bernhard, Lagnel, Jacques, Loire, Etienne, Parrinello, Hugues, Severac, Dany, Lopez-Roques, Celine, Donnadieu, Cecile, Manno, Maxime, Berges, Helene, Gharbi, Karim, Lawson-Handley, Lori, Zang, Lian-Sheng, Vogel, Heiko, Estoup, Arnaud, and Prud’homme, Benjamin

Published
2018
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23. Genome sequence of the cluster root forming white lupin;

Author

Hufnagel, Barbara, Marques, André, Soriano, Alexandre, Marquès, Laurence, Divol, Fanchon, Doumas, Patrick, Sallet, Erika, Mancinotti, Davide, Carrere, Sebastien, Marande, William, Arribat, Sandrine, Keller, Jean, Huneau, Cecile, Blein, Thomas, Aime, Delphine, Laguerre, Malika, Taylor, Jemma, Schubert, Veit, Nelson, Matthew, Geu-Flores, Fernando, Crespi, Martin, Gallardo-Guerrero, Karine, Delaux, Pierre-Marc, Salse, Jerome, Berges, Helene, Guyot, Romain, Gouzy, Jerome, and PERET, Benjamin

Subjects
Vegetal Biology, lupinus albus, absorption azotée, aliment sans gluten, racine laterale, Biologie végétale, nutrition protéique
Abstract

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1–5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify the APETALA2 transcription factor LaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.

Published
2019

24. Identifications des gènes sous-jacents à un QTL de tolérance au gel chez le pois

Author

Beji, Sana, Kreplak, Jonathan, Aubert, Gregoire, Vautrin, Sonia, Bellec, Arnaud, Berges, Helene, Bahrman, Nasser, Lejeune-Henaut, Isabelle, Delbreil, Bruno, Agroressources et Impacts environnementaux (AgroImpact), Institut National de la Recherche Agronomique (INRA), Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre National de Ressources Génomiques Végétales (CNRGV), Institut Charles Viollette (ICV) - EA 7394 (ICV), Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de la Recherche Agronomique (INRA)-Université d'Artois (UA)-Institut Supérieur d'Agriculture, Institut National de la Recherche Agronomique (INRA). FRA., ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Université d'Artois (UA)-Institut National de la Recherche Agronomique (INRA)-Université du Littoral Côte d'Opale (ULCO)-Institut Supérieur d'Agriculture-Université de Lille

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

Prod 2018-220o BAP GEAPSI INRA; National audience

Published
2018

25. Genome sequence of white lupin, a model to study root developmental adaptations

Author

Hufnagel, Barbara, Marques, André, MARANDE, William, Sallet, Erika, Sorriano, Alexandre, Arribat, Sandrine, Berges, Helene, Gouzy, Jerome, PERET, Benjamin, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Développement et Plasticité du Système Racinaire (PLASTICITE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
racine, lupinus albus, lupinus angustifolius, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, medicago truncatula, root, organisation génomique
Abstract

White lupin ( Lupinus albus ; 2n=50) stands out as a model legume species since it is the only crop producing cluster roots, one of the most outstanding developmental adaptations to nutrient‐scarce environments. We report a high‐quality chromosome‐scale assembly of white lupin genome, together with an extensive transcriptome data from ten different organs of that species. We took advantage of single‐molecule real‐time technology, in combination with short‐reads sequencing and optical and genetic maps in order to have a successful assembly. The final assembly size is 451Mb with a N50 of 17Mb. About 96% (434Mb) of the assembled genome is included on the 25 pseudo‐chromosomes. The structural annotation identified 38 258 coding genes and 3129 ncRNA, being 97.3% genes anchored on the pseudo‐chromosomes. A majority (94.6%) of the 1440 genes in the Plantae BUSCO dataset were identified in the annotation, which is suggestive of a complete assembly and annotation. White lupin genome revealed to be laden with gene duplications and repetitive elements. It presents extensive duplication blocks inside its own genome and also a high degree of synteny with the close legumes species Lupinus angustifolious and Medicago truncatula . This genome is a valuable resource and represents a keystone for legumes genomics research.

Published
2018

26. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions

Author

Sforça, Danilo Augusto, primary, Vautrin, Sonia, additional, Cardoso-Silva, Claudio Benicio, additional, Mancini, Melina Cristina, additional, Romero-da Cruz, María Victoria, additional, Pereira, Guilherme da Silva, additional, Conte, Mônica, additional, Bellec, Arnaud, additional, Dahmer, Nair, additional, Fourment, Joelle, additional, Rodde, Nathalie, additional, Van Sluys, Marie-Anne, additional, Vicentini, Renato, additional, Garcia, Antônio Augusto Franco, additional, Forni-Martins, Eliana Regina, additional, Carneiro, Monalisa Sampaio, additional, Hoffmann, Hermann Paulo, additional, Pinto, Luciana Rossini, additional, Landell, Marcos Guimarães de Andrade, additional, Vincentz, Michel, additional, Berges, Helene, additional, and de Souza, Anete Pereira, additional

Published
2019
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27. Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.)

Author

Gali, Krishna Kishore, primary, Tar’an, Bunyamin, additional, Madoui, Mohammed-Amin, additional, van der Vossen, Edwin, additional, van Oeveren, Jan, additional, Labadie, Karine, additional, Berges, Helene, additional, Bendahmane, Abdelhafid, additional, Lachagari, Reddy V. B., additional, Burstin, Judith, additional, and Warkentin, Tom, additional

Published
2019
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28. Oak genome reveals facets of long lifespan

Author

Leroy, Thibault, Murat, Florent, Duplessis, Sébastien, Faye, Sébastien, Francillonne, Nicolas, Labadie, Karine, Le Provost, Grégoire, Lesur Kupin, Isabelle, Bartholome, Jérôme, Faivre-Rampant, Patricia, Kohler, Annegret, Leplé, Jean-Charles, Chantret, Nathalie, Chen, Jun, Dievart, Anne, Alaeitabar, Tina, Barbe, Valérie, Belser, Caroline, Berges, Helene, Bodenes, Catherine, Bogeat-Triboulot, Marie-Béatrice, Bouffaud, Marie-Lara, Brachi, Benjamin, Chancerel, Emilie, Cohen, David, Couloux, Arnaud, Da Silva, Corinne, Dossat, Carole, Ehrenmann, François, Gaspin, Christine, Grima-Pettenati, Jacqueline, Guichoux, Erwan, Hecker, Arnaud, Herrmann, Sylvie, Hugueney, Philippe, Hummel, Iréne, Klopp, Christophe, Lalanne, Céline, Lascoux, Martin, Lasserre, Eric, Lemainque, Arnaud, Desprez-Loustau, Marie Laure, Luyten, Isabelle, Madoui, Mohammed-Amin, Mangenot, Sophie, Marchal, Clémence, Maumus, Florian, Mercier, Jonathan, Michotey, Célia, Panaud, Olivier, Picault, Nathalie, Rouhier, Nicolas, Rué, Olivier, Rustenholz, Camille, Salin, Franck, Soler, Marçal, Tarkka, Mika, Velt, Amandine, Zanne, Amy E., Martin, Francis, Wincker, Patrick, Quesneville, Hadi, Kremer, Antoine, Salse, Jerome, Plomion, Christophe, Aury, Jean-Marc, and Amselem, Joelle

Subjects
Forestry, Genomics, Plant evolution, Plant Immunity, Sequencing
Abstract

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Published
2018

29. FANCM Limits Meiotic Crossovers in Brassica Crops

Author

Blary, Aurélien, Gonzalo, Adrián, Eber, Frederique, Berard, Aurélie, Berges, Helene, Bessoltane, Nadia, Charif, Delphine, Charpentier, Catherine, Cromer, Laurence, Fourment, Joelle, Genevriez, Camille, Le Paslier, Marie-Christine, Lodé-Taburel, Maryse, Lucas, Marie-Odile, Nesi, Nathalie, Lloyd, Andrew, Chèvre, Anne-Marie, Jenczewski, Eric, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Ecology and Evolution, Université de Lausanne = University of Lausanne (UNIL), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), ANR-14-CE19-0004 - CROC, INRA BAP division (Appel a Manifestation d'interet, HyperRec), LabEx Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], PIOF-GA-2013-628128 POLYMEIO, ANR-14-CE19-0004,CROC,Contrôle de la fréquence de recombinaison méiotique pour accélérer l'innovation variétales chez les espèces cultivées polyploïdes(2014), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), European Project: 606956,EC:FP7:PEOPLE,FP7-PEOPLE-2013-ITN,COMREC(2013), Université de Lausanne (UNIL), 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
méiose, Vegetal Biology, FANCM, brassica, meiotic crossover, TILLING, plant breeding, polyploidy, Translational biology, arabidopsis thaliana, fungi, Correction, food and beverages, Plant Science, lcsh:Plant culture, variation génétique, brassica napus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, mutation, Biologie végétale, Original Research, sélection végétale
Abstract

International audience; Meiotic crossovers (COs) are essential for proper chromosome segregation and the reshuffling of alleles during meiosis. In WT plants, the number of COs is usually small, which limits the genetic variation that can be captured by plant breeding programs. Part of this limitation is imposed by proteins like FANCM, the inactivation of which results in a 3-fold increase in COs in Arabidopsis thaliana. Whether the same holds true in crops needed to be established. In this study, we identified EMS induced mutations in FANCM in two species of economic relevance within the genus Brassica. We showed that CO frequencies were increased in fancm mutants in both diploid and tetraploid Brassicas, Brassica rapa and Brassica napus respectively. In B. rapa, we observed a 3-fold increase in the number of COs, equal to the increase observed previously in Arabidopsis. In B. napus we observed a lesser but consistent increase (1.3-fold) in both euploid (AACC) and allohaploid (AC) plants. Complementation tests in A. thaliana suggest that the smaller increase in crossover frequency observed in B. napus reflects residual activity of the mutant C copy of FANCM. Altogether our results indicate that the anti-CO activity of FANCM is conserved across the Brassica, opening new avenues to make a wider range of genetic diversity accessible to crop improvement.

Published
2018
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30. Oak genome reveals facets of long lifespan

Author

Plomion, Christophe, Aury, Jean-Marc, Amselem, Joelle, Leroy, Thibault, Murat, Florent, Duplessis, Sébastien, Faye, Sébastien, Francillonne, Nicolas, Labadie, Karine, Le Provost, Grégoire, Lesur Kupin, Isabelle, Bartholome, Jérôme, Faivre-Rampant, Patricia, Kohler, Annegret, Leplé, Jean-Charles, Chantret, Nathalie, Chen, Jun, Dievart, Anne, Alaeitabar, Tina, Barbe, Valérie, Belser, Caroline, Berges, Helene, Bodenes, Catherine, Bogeat-Triboulot, Marie-Béatrice, Bouffaud, Marie-Lara, Brachi, Benjamin, Chancerel, Emilie, Cohen, David, Couloux, Arnaud, da Silva, Corinne, Dossat, Carole, Ehrenmann, François, Gaspin, Christine, Grima Pettenati, Jacqueline, Guichoux, Erwan, Hecker, Arnaud, Herrmann, Sylvie, Hugueney, Philippe, Hummel, Irène, Klopp, Christophe, Lalanne, Céline, Lascoux, Martin, Lasserre, Eric, Lemainque, Arnaud, Desprez-Loustau, Marie Laure, Luyten, Isabelle, Madoui, Mohammed-Amin, Mangenot, Sophie, Marchal, Clémence, Maumus, Florian, Mercier, Jonathan, Michotey, Célia, Panaud, Olivier, Picault, Nathalie, Rouhier, Nicolas, Rué, Olivier, Rustenholz, Camille, Salin, Franck, Soler, Marçal, Tarkka, Mika, Velt, Amandine, Zanne, Amy E., Martin, Francis, Wincker, Patrick, Quesneville, Hadi, Kremer, Antoine, Salse, Jerome, 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), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Etude du Polymorphisme des Génomes Végétaux (EPGV), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Centre National de Ressources Génomiques Végétales (CNRGV), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Department of Soil Ecology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Régulation et Dynamique de la Formation du Bois, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), German Centre for Integrative Biodiversity Research, Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratori del Suro, Universitat de Girona (UdG), Department of Biological Sciences, University at Albany [SUNY], State University of New York (SUNY)-State University of New York (SUNY), 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 d'Evry Val d'Essonne, Université Paris-Saclay, European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), German Centre for Integrative Biodiversity Research (iDiv), The George Washington University (GW), Université d'Évry-Val-d'Essonne (UEVE), 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 Strasbourg (UNISTRA)-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), Biodiversité, Gènes et Communautés, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), SILVA (SILVA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Lorraine (UL), Helmholtz Centre for Environmental Research (UFZ), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)-AgroParisTech

Subjects
Evolutionary Biology, DNA, Plant, [SDV]Life Sciences [q-bio], Longevity, Genetic Variation, Forestry, Sequence Analysis, DNA, Genomics, Biological Evolution, Article, Evolutionsbiologi, Quercus, Plant evolution, Mutation, Genetics, Sequencing, Plant Immunity, Genetik, Genome, Plant, Phylogeny
Abstract

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Published
2018
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31. A mosaic monoploid reference sequence for the highly complex genome of sugarcane

Author

Garsmeur, Olivier, Droc, Gaetan, Antonise, Rudie, Grimwood, Jane, Potier, Bernard, Aitken, Karen, Jenkins, Jerry, Martin, Guillaume, Charron, Carine, Hervouet, Catherine, Costet, Laurent, Yahiaoui, Nabila, Healey, Adam, Sims, David, Cherukuri, Yesesri, Sreedasyam, Avinash, Kilian, Andrzej, Chan, Agnes, Van Sluys, Marie-Anne, Swaminathan, Kankshita, Town, Christopher, Berges, Helene, Simmons, Blake, Glaszmann, Jean Christophe, van der Vossen, Edwin, Henry, Robert, Schmutz, Jeremy, D’Hont, Angélique, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Montpellier (UM), Keygene N.V., HudsonAlpha Institute for Biotechnology [Huntsville, AL], South African Sugarcane Research Institute, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Diversity Arrays Technology Pty Ltd (DArT P/L), J. Craig Venter Institute [La Jolla, USA] (JCVI), Universidade Federal de São Paulo, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Joint BioEnergy Institute, University of Queensland [Brisbane], Joint Genome Institute (JGI), International Consortium for Sugarcane Biotechnology, South Green Bioinformatics platform, Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], Lawrence Berkeley National Laboratory, 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
Chromosomes, Artificial, Bacterial, F30 - Génétique et amélioration des plantes, Models, lcsh:Science, Génétique, Vegetal Biology, Genome, Saccharum officinarum, Mosaicism, Bacterial, food and beverages, Single Nucleotide, Saccharum, Artificial, Sequence Analysis, Genome, Plant, Biotechnology, Science, Polymorphism, Single Nucleotide, Chromosomes, Chromosomes, Plant, Article, Genetic, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Variété, Polymorphism, Sorghum, Saccharum spontaneum, Ploidies, Génome, Base Sequence, Models, Genetic, Human Genome, Gene Amplification, Plant, DNA, Sequence Analysis, DNA, Amélioration des plantes, Genomic Structural Variation, DNA Transposable Elements, lcsh:Q, Biologie végétale, canne à sucre, polyploïdisation
Abstract

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence., Sugarcane (Saccharum spp.) is a crop of major economic significance but has complex genome structure. Here, the authors generate a BAC-based monoploid sugarcane reference sequence.

Published
2018
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32. The pea genome

Author

Kreplak, Jonathan, Madoui, Mohammed-Amin, Labadie, Karine, Aubert, Gregoire, Bayer, Philippe, Capal, P., Klein, Anthony, KOUGBEADJO, Ayité, Vrana, J., Gali, K.K., Fournier, Carine, d'Agata, Léo, Taran, B., Belser, C., Le Paslier, Marie-Christine, Bendahmane, Abdelhafid, Berges, Helene, Barbe, Valérie, McGee, Rebecca, Lichtenzveig, Judith, Coyne, Clarice J., Warkentin, Tom D., Batley, J., Macas, Jiří, Edwards, Dave, Dolezel, Jaroslav, Wincker, Patrick, Burstin, Judith, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Bayer Cropscience, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), 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), Centre National de Ressources Génomiques Végétales (CNRGV), USDA-ARS : Agricultural Research Service, Molecular Biology, Bioinformatics, Evolutionary Biology, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), University of Western Australia, Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), School of Plant Biology, The University of Western Australia (UWA), and Noble Research Institute.

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

International audience; The International Pea Genome Consortium Pea (Pisum sativum L.) has long been a model for plant genetics. It is also a widely grown pulse crop producing protein-rich seeds in a sustainable manner. Thanks to large national and international programs, and driven by innovations in sequencing technology, informatics and biotechnology, many genomic resources are now available for pea. An atlas of the expression of its genes in many tissues, high density genetic mapping, and the ongoing sequencing of its genome have provided useful tools for dissecting traits of interest. We will present how the pea genome draft sequence opens the way to explore genetic diversity of pea.

Published
2017

33. Stb16q-mediated resistance against Zymoseptoria tritici is conferred by a new class of R gene

Author

Saintenac, Cyrille, Cambon, Florence, Faris, Justin, Xu, Steven, Marande, William, Berges, Helene, Ghaffary, Mahmod Tabib, Aouini, Lamia, Kema, Gert Hj, Robert, Olivier, Langin, Thierry, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Cereal Crops Research Unit, USDA-ARS : Agricultural Research Service, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Seed and Plant Improvement Research Department, Agricultural Research, Education and Extension Organisation (AREEO ), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Florimond Desprez, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), United States Department of Agriculture - Agricultural Research Service, Wageningen University and Research Centre [Wageningen] (WUR), ProdInra, Archive Ouverte, and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)

Subjects
[SDV] Life Sciences [q-bio], blé, wheat, [SDV]Life Sciences [q-bio]
Abstract

Book of abstracts p. 61 ISBN: 978-3-900932-48-0Book of abstracts p. 61ISBN: 978-3-900932-48-0; Stb16q-mediated resistance against Zymoseptoria tritici is conferred by a new class of R gene. 13. International Wheat Genetics Symposium

Published
2017

34. Development of a sequence-based reference physical map of pea (Pisum sativum L.)

Author

Kishore Gali, Krishna, primary, Tar’an, Bunyamin, additional, Madoui, Mohammed-Amin, additional, van der Vossen, Edwin, additional, Oeveren, Jan van, additional, Labadie, Karine, additional, Berges, Helene, additional, Bendahmane, Abdelhafid, additional, Lachagari, Reddy V.B., additional, Burstin, Judith, additional, and Warkentin, Tom, additional

Published
2019
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35. Isolation and characterization of a priB mutant of Escherichia coli influencing plasmid copy number of deltarop ColE1-type plasmids

Author

Berges, Helene, Oreglia, Jacqueline, Joseph-Liauzun, Evelyne, and Fayet, Olivier

Subjects
Plasmids -- Genetic aspects, Microbial mutation -- Genetic aspects, Escherichia coli -- Genetic aspects, Biological sciences
Abstract

The effect of plasmid copy number of a priB mutant of Escherichia coli was analyzed during the replication of ColE1-related plasmids in vivo. Analysis of the OFB3085 human granulocyte-macrophage colony stimulating factor (hGM-CSF)-tolerant mutant strain indicated the role of PriB in mediating the replication of plasmids. Furthermore, the mutation carried by the OFB3085 strain significantly reduced the copy number of the plasmids.

Published
1997

36. Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane

Author

Sforça, Danilo Augusto, primary, Vautrin, Sonia, additional, Cardoso-Silva, Claudio Benicio, additional, Mancini, Melina Cristina, additional, da Cruz, María Victoria Romero, additional, da Silva Pereira, Guilherme, additional, Conte, Mônica, additional, Bellec, Arnaud, additional, Dahmer, Nair, additional, Fourment, Joelle, additional, Rodde, Nathalie, additional, Van Sluys, Marie-Anne, additional, Vicentini, Renato, additional, Garcia, Antônio Augusto Franco, additional, Forni-Martins, Eliana Regina, additional, Carneiro, Monalisa Sampaio, additional, Hoffmann, Hermann Paulo, additional, Pinto, Luciana Rossini, additional, de Andrade Landell, Marcos Guimarães, additional, Vincentz, Michel, additional, Berges, Helene, additional, and Souza, Anete Pereira, additional

Published
2018
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37. The genomic basis of colour pattern polymorphism in the harlequin ladybird

Author

Gautier, Mathieu, primary, Yamaguchi, Junichi, additional, Foucaud, Julien, additional, Loiseau, Anne, additional, Ausset, Aurélien, additional, Facon, Benoit, additional, Gschloessl, Bernhard, additional, Lagnel, Jacques, additional, Loire, Etienne, additional, Parrinello, Hugues, additional, Severac, Dany, additional, Lopez-Roques, Celine, additional, Donnadieu, Cecile, additional, Manno, Maxime, additional, Berges, Helene, additional, Gharbi, Karim, additional, Lawson-Handley, Lori, additional, Zang, Lian-Sheng, additional, Vogel, Heiko, additional, Estoup, Arnaud, additional, and Prud’homme, Benjamin, additional

Published
2018
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38. Stb6 is a Wall-Associated Kinase Gene that provides Gene-for-Gene Resistance against Zymoseptoria tritici in Wheat

Author

Saintenac, Cyrille, Lee, Wing-Sham, Cambon, Florence, Rudd, Jason J., King, Robert, MARANDE, William, Berges, Helene, Phillips, Andy L., Uauy, Cristobal, Hallond-Kosack, Kim, Langin, Thierry, Kanyuka, Kostya, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Rothamsted Research, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), John Innes Centre, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Biotechnology and Biological Sciences Research Council (BBSRC), John Innes Centre [Norwich], and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

Subjects
blé, kinase, wheat, gène, [SDV]Life Sciences [q-bio], food and beverages, genes
Abstract

W975W975; Septoria tritici blotch (STB) is a devastating foliar disease of wheat encountered in most wheat growing areas of the world resulting from infection by the ascomycete fungus Zymoseptoria tritici. Emergence and dispersal of fungicide resistance in Z. tritici field populations seriously threatens wheat production, therefore STB resistance breeding is considered a high priority. To date, 21 major genes conferring isolate-specific resistance as well as 89 resistance QTLs have been characterized genetically. However, none of these have as yet been cloned and mechanisms of resistance remain poorly understood. Here, we report isolation of the Stb6 gene controlling resistance to Z. tritici isolates carrying the matching AvrStb6 gene. This wheat gene confers a semi-dominant resistance to Z. tritici, which does not involve induction of HR. Fine-mapping using a large F2 mapping population derived from a cross between the resistant wheat Chinese Spring (Stb6) and the susceptible wheat Courtot and subsequent BAC and genomic DNA contigs sequence analysis revealed a cluster of wall-associated receptor kinase (WAK) like genes. Using VIGS, TILLING and genetic complementation, we demonstrated that one of these candidates corresponds to Stb6. Disease susceptibility in Courtot results most likely from a point-mutation in the Stb6 kinase domain leading to a loss of defense signaling. Stb6 allele mining revealed an ancient origin of this gene and the predominance of a major resistance haplotype. Furthermore, genotyping a large wheat collection using diagnostic markers showed that Stb6 is present in nearly half of European cultivated wheat. Stb6 is the first gene to be cloned that confers resistance to the STB disease. Isolation of this gene is the first step toward in depth characterization of the wheat - Z. tritici molecular interactions.

Published
2017

39. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Author

BADOUIN, Hélène, Gouzy, Jerome, GRASSA, Christopher, Murat, Florent, Staton, S Evan, Cottret, Ludovic, Lelandais-briere, Christine, Owens, Gregory L, Carrere, Sebastien, mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C, Bowers, John E, Hubner, Sariel, Bellec, Arnaud, Berard, Aurélie, Berges, Helene, BLANCHET, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Cecile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J, Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, LORENZON, Lolita, Mandel, Jennifer R, Marage, Gwenola, MARCHAND, Gwenaëlle, MARQUAND, Elodie, MESTRIES, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot - Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Céline, Vares, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M, Salse, Jerome, Munos, Stephane, Vincourt, Patrick, Rieseberg, Loren H, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Botany and Biodiversity Research Centre, University of British Columbia (UBC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Department of Plant Biology, Miller Plant Sciences, University of Georgia [USA], Department of Biotechnology, Tel-Hai Academic College, Galilee Research Institute (Migal), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Dow AgroSciences LLC, Biogemma, GeT PlaGe, Genotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Department of Plant Sciences, University of California, Department of Biology, Northern Arizona University [Flagstaff], Center for Genomics and Bioinformatics, Indiana University [Bloomington], Indiana University System-Indiana University System, Department of Biological Sciences, The Open University [Milton Keynes] (OU), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Department of Horticulture, University of Wisconsin-Madison, The Wellcome Trust Sanger Institute [Cambridge], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), French National Research Agency : SUNYFUEL/ANR-07-GPLA-0022, SUNRISE/ANR-11-BTBR-0005 Midi-Pyrenees Region, European Fund for Regional Development, French Fund for Competitiveness Clusters (FUI), Genoscope SystemSun project, Genome Canada, Genome BC's Applied Genomics Research in Bioproducts or Crops (ABC) Competition, NSF Plant Genome Program : DBI-082045, International Consortium for Sunflower Genomics Resources, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), 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), Tel-Hai College, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-07-GPLA-0022,SUNYFUEL,Improving sunflower yield and quality for biofuel production by genomics and genetics(2007), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Galilee Research Institute [Israël] (MIGAL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of California (UC), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), University of British Columbia ( UBC ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut National de la Recherche Agronomique ( INRA ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Department of Ecology and Evolutionary Biology ( Faculty of Biology ), University of Georgia, Galilee Research Institute ( Migal ), Centre National de Ressources Génomiques Végétales ( CNRGV ), Institut National de la Recherche Agronomique ( INRA ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, The Open University [Milton Keynes] ( OU ), University of Wisconsin-Madison [Madison], Wellcome Trust Sanger Institute, and Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA )

Subjects
[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, sunflower, Acclimatization, résistance au stress, génome végétal, Flowers, genome evolution, résilience, Evolution, Molecular, Gene Expression Regulation, Plant, Stress, Physiological, Gene Duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Oils, Sunflower Oil, genome, food and beverages, Genetic Variation, Genomics, Sequence Analysis, DNA, tournesol, genêtic variation, stress biotique, diversité génétique, Helianthus, Transcriptome, Genome, Plant
Abstract

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

Published
2016
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40. Towards the genome sequence of pea : a tribute to Mendel

Author

Madoui , Mohammed-Amin, Labadie , K., Kreplak , Jonathan, Aubert , Gregoire, d'Agata , Léo, Capal , P., Fournier , Carine, KOUGBEADJO , Ayité, Vrana , J., Gali , K., Taran , B., Belser , C., Le Paslier , Marie-Christine, McGee , Rebecca, Edwards , D., Batley , J., Bendahmane , Abdelhafid, Berges , Helene, Barbe , V., Tayeh , Nadim, Klein , Anthony, Lichtenzveig , Judith, Aury , J-M., Coyne , C.J., Warkentin , T., Dolezel , J., Wincker , P., Burstin , Judith, 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), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Grain Legume Genetics Physiology Research, USDA-ARS : Agricultural Research Service, The University of Western Australia (UWA), 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), Centre National de Ressources Génomiques Végétales (CNRGV), Molecular Biology, Bioinformatics, Evolutionary Biology, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Western Region Plant Introduction Station, Legume Society., 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, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institute of Experimental Botany ASCR, 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 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), Génoscope, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), University of Saskatchewan [Saskatoon] ( U of S ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), USDA-ARS, University of Western Australia, UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Centre National de Ressources Génomiques Végétales ( CNRGV ), and Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC )

Subjects
pea, genome, sequence, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], food and beverages
Abstract

BAP GEAPSI BAP GEAPSIBAPGEAPSI; Pea (Pisum sativum L.) was the original model organism for Mendel´s discovery of the laws of inheritance and kept this model status until the advent of molecular biology at the end of the 20th century. Pea is also one of the world’s oldest domesticated crops. It is currently the third most widely grown pulse crop, as its seeds serve as a protein-rich food for humans and livestock alike. While several legume species genome's draft sequences have been produced, progress in pea genomics has lagged behind largely as a consequence of its complex and large genome size. The pea genome is large (ca 4.45 Gb), probably resulting from recent expansion of retrotransposons followed by sequence diversification. The Pea Genome International Project has undertaken several complementary strategies in order to produce a high-quality draft sequence of the species. We will present how this draft sequence opens the way to renew strategies in pea breeding.

Published
2016

41. Unlocking the cross-incompatibility between wheat and rye?

Author

Lesage, Véronique, Alfares, Walid, Gerjets, Tanja, Vautrin, Sonia, Berges, Helene, Choulet, Frédéric, Feuillet, Catherine, Sourdille, Pierre, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), and International Association of Sexual Plant Reproduction Research (IASPRR). RUS.

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

Événement(s) lié(s) : - 4. Frontiers of sexual plant reproduction; International audience

Published
2016

42. Sequencing and Analysis of Wheat Chromosome 1B

Author

Choulet, Frédéric, Rimbert, Hélène, JOSSELIN, Ambre-Aurore, Darrier, Benoît, Sourdille, Pierre, Balfourier, Francois, Barbe, Valérie, Alberti, Adriana, Labadie, Karine, Mangenot, Sophie, Couloux, Arnaud, Wincker, Patrick, Berges, Helene, Alaux, Michael, Letellier, Thomas, Quesneville, Hadi, Frenkel, Zeev, Fahima, Tzion, Korol, Abraham, Paux, Etienne, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), 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), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Institute of Evolution, University of Haifa, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], food and beverages
Abstract

We are currently producing a reference sequence of the bread wheat chromosome 1B (535 Mb) by sequencing 6023 BAC clones comprising the minimal tilling path of the physical maps of both short and long arms. BACs were sequenced by pools using a combination of Illumina MiSeq paired-end reads and HiSeq2500 5 kb mate pairs. First round of assembly yielded 7131 scaffolds representing 534 Mb. Report on the improvement of this assembly, the construction of a pseudomolecule and the comparison with the previous sequencing and assembly of chromosome 3B will be presented.

Published
2016

43. Exploitation of the 5BS physical map to complete the SKr crossability locus

Author

Lesage, Véronique, Choulet, Frédéric, Vautrin, Sonia, Salina, Elena A., Debote, Marie-Claire, Charef, Bouzid, Berges, Helene, Feuillet, Catherine, Sourdille, Pierre, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Russian Academy of Sciences [Moscow] (RAS), CropScience, Bayer, and Scherago International Inc.. USA.

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

International audience

Published
2016

44. Physical Map of the Short Arm of Bread Wheat Chromosome 3D

Author

Holušová, Kateřina, primary, Vrána, Jan, additional, Šafář, Jan, additional, Šimková, Hana, additional, Balcárková, Barbora, additional, Frenkel, Zeev, additional, Darrier, Benoit, additional, Paux, Etienne, additional, Cattonaro, Federica, additional, Berges, Helene, additional, Letellier, Thomas, additional, Alaux, Michael, additional, Doležel, Jaroslav, additional, and Bartoš, Jan, additional

Published
2017
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45. Genome discovery of deep frost-tolerant eucalyptus for breeding and molecular ecology

Author

Harvengt, Luc, San Clemente, Hélène, Gion, Jean-Marc, Klopp, Christophe, Berges, Helene, Potts, Brad M., Vaillancourt, Rene E., Marque, Christiane, Teulières, Chantal, Grima-Pettenati, Jacqueline, Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA), Université Fédérale Toulouse Midi-Pyrénées, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), and University of Tasmania [Hobart, Australia] (UTAS)

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

National audience

Published
2015

46. Development of Sinorhizobium meliloti pilot macroarrays for transcriptome analysis

Author

Berges, Helene, Lauber, Emmanuelle, Liebe, Carine, Batut, Jacques, Kahn, Daniel, de Bruijn, Frans J., and Ampe, Frederic

Subjects
Host-bacteria relationships -- Genetic aspects, Host-bacteria relationships -- Analysis, Genomes -- Analysis, Gene expression -- Analysis, DNA -- Analysis, Biological sciences
Abstract

Research describes the designing of DNA macroarrays of Sinorhizobium meliloti genes and testing them in the bacteium's gene expression process. Thirtyfour regulatory genes are used in the construction of macroarrays to assess the length of the polymerase chain reaction products, the influence of of the 5' tag of the primers, and RNA labeling method.

Published
2003

47. The first insight into the Salvia (Lamiaceae) genome via BAC library construction and high-throughput sequencing of target BAC clones

Author

Hao, Da Cheng, Vautrin, Sonia, Song, Chi, Zhu, Ying Jie, Berges, Helene, Sun, Chao, Chen, Shi Lin, Dalian Jiaotong University, Partenaires INRAE, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Institute of medicinal plant development, Chinese Academy of Medical Sciences, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, China Scholarship Council [201208210122], and Ministry of Science and Technology national support program [2012BAI29B01]

Subjects
Genome characterization, High-throughput sequencing, [SDV]Life Sciences [q-bio], Microsatellite, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gridded BAC library, Salvia officinalis, Terpene synthase
Abstract

International audience; Salvia is a representative genus of Lamiaceae, a eudicot family with significant species diversity and population adaptibility. One of the key goals of Salvia genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of medicinal plants to increase their health and productivity. Large-insert genomic libraries are a fundamental tool for achieving this purpose. We report herein the construction, characterization and screening of a gridded BAC library for Salvia officinalis (sage). The S. officinalis BAC library consists of 17,764 clones and the average insert size is 107 Kb, corresponding to similar to 3 haploid genome equivalents. Seventeen positive clones (average insert size 115 Kb) containing five terpene synthase (TPS) genes were screened out by PCR and 12 of them were subject to Illumina HiSeq 2000 sequencing, which yielded 28,097,480 90-bp raw reads (2.53 Gb). Scaffolds containing sabinene synthase (Sab), a Sab homolog, TPS3 (kaurene synthase-like 2), copalyl diphosphate synthase 2 and one cytochrome P450 gene were retrieved via de novo assembly and annotation, which also have flanking noncoding sequences, including predicted promoters and repeat sequences. Among 2,638 repeat sequences, there are 330 amplifiable microsatellites. This BAC library provides a new resource for Lamiaceae genomic studies, including microsatellite marker development, physical mapping, comparative genomics and genome sequencing. Characterization of positive clones provided insights into the structure of the Salvia genome. These sequences will be used in the assembly of a future genome sequence for S. officinalis.

Published
2015

48. SKr, a major QTL involved in crossability of wheat with rye

Author

Lesage, Véronique S., Alfares, Walid, Gerjets, Tanja, Vautrin, Sonia, Berges, Helene, Choulet, Frédéric, Feuillet, Catherine, Sourdille, Pierre, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

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

International audience

Published
2014

49. Assembling a pseudomolecule for a wheat chromosome: the 3B experience

Author

Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Theil, Sébastien, Sourdille, Pierre, Balfourier, François, Aury, Jean-Marc, Berges, Helene, Dolezel, Jaroslav, Quesneville, Hadi, Wincker, Patrick, Feuillet, Catherine, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Czech Academy of Sciences [Prague] (CAS), Unité de Recherche Génomique Info (URGI), 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), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)

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

International audience; We produced a reference sequence for the giant wheat chromosome 3B (900 Mb). The strategy established was based on the sequencing of 8452 BACs pooled by 10 using Roche/454 8 kb long paired-end reads combined with Illumina whole 3B shotgun (2x100 bp reads). Automated assembly, manual improvement of the scaffolding, gap filling, and BAC redundancy removal led to assemble 2808 scaffolds representing 833 Mb, estimated to cover 94% of the chromosome. The scaffold N50 was 949 kb and gaps represented only 7% of the sequence. Additionally, SNP markers were developed and genotyped in a mapping population and association panels. A high-density genetic map was constructed and marker positions were refined using Linkage Disequilibrium data. This allowed the construction of a single pseudomolecule comprised of 1358 ordered scaffolds representing 774 Mb i.e. 93% of the sequence.

Published
2014

50. A reference sequence of wheat chromosome 3B

Author

Choulet, Frédéric, Alberti, Adriana, Theil, Sébastien, Glover, Natasha Marie, Barbe, Valérie, Daron, Josquin, Pingault, Lise, Sourdille, Pierre, Couloux, Arnaud, Paux, Etienne, Leroy, Philippe, Mangenot, Sophie, Guilhot, Nicolas, Le Gouis, Jacques, Balfourier, Francois, Alaux, Michael, Jamilloux, Veronique, Poulain, Julie, Duran, Céline, Bellec, Arnaud, Gaspin, Christine, Safar, Jan, Dolezel, Jaroslav, Roger, Jane, Vandepoele, Kent, Aury, Jean-­‐Marc, Mayer, Klaus, Berges, Helene, Quesneville, Patrick, Wincker, P., and Feuillet, Catherine

Subjects
chromosome 3B, Vegetal Biology, génomique comparative, blé hexaploïde, Biologie végétale
Published
2014

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