1. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release
- Author
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Jean-Charles Leplé, Céline Noirot, Antoine Kremer, Christian Burban, Hadi Quesneville, Michael Stierschneider, Valérie Léger, Saneyoshi Ueno, Pascal Bento, Corinne Da Silva, François Buscot, Silvia Fluch, Jérôme Bartholomé, Christophe Plomion, Christophe Klopp, Jean-Marc Aury, François Ehrenmann, Isabelle Lesur, Lasse Feldhahn, Joelle Amselem, Céline Lalanne, Florent Murat, Mika T. Tarkka, Jérôme Salse, Caroline Belser, Sylvie Herrmann, Grégoire Le Provost, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Biométrie et Intelligence Artificielle (UBIA), 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), Austrian Institute of Technology [Vienna] (AIT), Department of Soil Ecology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), German Centre for Integrative Biodiversity Research, Synthetic and Systems Biology Unit [Szeged], Biological Research Centre [Szeged] (BRC), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Biodiversité, Gènes et Communautés, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Helmholtz Centre for Environmental Research (UFZ), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)
- Subjects
0106 biological sciences ,[SDV]Life Sciences [q-bio] ,Phénotype ,Sequence assembly ,UniGene ,comparative genomics ,01 natural sciences ,Genome ,F30 - Génétique et amélioration des plantes ,Gene Expression Regulation, Plant ,bud phenology ,K01 - Foresterie - Considérations générales ,genomic features [EN] ,ComputingMilieux_MISCELLANEOUS ,Genetics ,0303 health sciences ,biology ,bourgeon ,Chromosome Mapping ,Plant Dormancy ,Adaptation, Physiological ,Quercus petraea ,quercus ,Quercus robur ,Phénologie ,Génotype ,Genome, Plant ,Research Article ,Biotechnology ,expression des gènes ,Genome evolution ,Genetic Speciation ,education ,fagaceae ,de novo assembly ,Séquence d'ARN ,03 medical and health sciences ,oak ,séquençage ,Gene ,030304 developmental biology ,transcriptome ,RNA-seq ,Comparative genomics ,Base Sequence ,Transcription génique ,Sequence Analysis, RNA ,génomique comparative ,15. Life on land ,biology.organism_classification ,dormance ,Evolutionary biology ,010606 plant biology & botany - Abstract
Background 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. Results 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. Conclusion 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1331-9) contains supplementary material, which is available to authorized users.
- Published
- 2015
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