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The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierINRA - Mathématiques et Informatique Appliquées [Unité MIAJ]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierMathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] [MaIAGE]
dc.contributor.authorBENTO, Pascal
hal.structure.identifierGénomique métabolique [UMR 8030]
dc.contributor.authorDA SILVA, Corinne
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorLEPLÉ, Jean-Charles
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorMURAT, Florent
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorUENO, Saneyoshi
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBARTHOLOME, Jérôme
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLALANNE, Céline
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorEHRENMANN, François
hal.structure.identifierUnité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) [UBIA]
dc.contributor.authorNOIROT, Celine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBURBAN, Christian
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLÉGER, Valérie
dc.contributor.authorAMSELEM, Joelle
hal.structure.identifierGenoscope - Centre national de séquençage [Evry] [GENOSCOPE]
dc.contributor.authorBELSER, Caroline
hal.structure.identifierUnité de Recherche Génomique Info [URGI]
dc.contributor.authorQUESNEVILLE, Hadi
hal.structure.identifierAustrian Institute of Technology [Vienna] [AIT]
dc.contributor.authorSTIERSCHNEIDER, Michael
hal.structure.identifierAustrian Institute of Technology [Vienna] [AIT]
dc.contributor.authorFLUCH, Silvia
dc.contributor.authorFELDHAHN, Lasse
hal.structure.identifierDepartment of Soil Ecology,
dc.contributor.authorTARKKA, Mika
hal.structure.identifierGerman Centre for Integrative Biodiversity Research
dc.contributor.authorHERRMANN, Sylvie
hal.structure.identifierSynthetic and Systems Biology Unit [Szeged]
dc.contributor.authorBUSCOT, Francois
hal.structure.identifierUnité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) [UBIA]
dc.contributor.authorKLOPP, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorSALSE, Jérôme
hal.structure.identifierUnité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) [UBIA]
dc.contributor.authorAURY, Jean-Marc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2015
dc.identifier.issn1471-2164
dc.description.abstractEn<strong>Background</strong> Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. <strong>Results</strong> The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. <strong>Conclusion</strong> In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
dc.language.isoen
dc.publisherBioMed Central
dc.subjecttranscriptome
dc.subjectcomparative genomics
dc.subjectbud phenology
dc.subject.enoak
dc.subject.ende novo assembly
dc.subject.enRNA-seq
dc.title.enThe oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release
dc.typeArticle de revue
dc.identifier.doi10.1186/s12864-015-1331-9
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalBMC Genomics
bordeaux.page112
bordeaux.volume16
bordeaux.issue1
bordeaux.peerReviewedoui
hal.identifierhal-02285504
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02285504v1
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