title: The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. ilesur@pierroton.inra.fr.|HelixVenture, F-33700, Mérignac, France. ilesur@pierroton.inra.fr.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Lesur
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. gregoire@pierroton.inra.fr.|University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France. gregoire@pierroton.inra.fr.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Le Provost
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France. pascal.bento@versailles.inra.fr.
authors.forename: Pascal
authors.initials: P
authors.lastname: Bento
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France. dasilva@genoscope.cns.fr.
authors.forename: Corinne
authors.initials: C
authors.lastname: Da Silva
authors.affiliation: INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075, Orléans, France. Jean-Charles.leple@orleans.inra.fr.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Leplé
authors.affiliation: INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France. florent.murat@clermont.inra.fr.
authors.forename: Florent
authors.initials: F
authors.lastname: Murat
authors.affiliation: Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan. saueno@ffpri.affrc.go.jp.
authors.forename: Saneyoshi
authors.initials: S
authors.lastname: Ueno
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. bartholo@pierroton.inra.fr.|CIRAD, UMR AGAP, F-34398, Montpellier, France. bartholo@pierroton.inra.fr.
authors.forename: Jerôme
authors.initials: J
authors.lastname: Bartholomé
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. lalanne@pierroton.inra.fr.|University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France. lalanne@pierroton.inra.fr.
authors.forename: Céline
authors.initials: C
authors.lastname: Lalanne
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. fehrenma@pierroton.inra.fr.|University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France. fehrenma@pierroton.inra.fr.
authors.forename: François
authors.initials: F
authors.lastname: Ehrenmann
authors.affiliation: Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France. Celine.Noirot@toulouse.inra.fr.
authors.forename: Céline
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authors.lastname: Noirot
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. Christian.Burban@pierroton.inra.fr.|University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France. Christian.Burban@pierroton.inra.fr.
authors.forename: Christian
authors.initials: C
authors.lastname: Burban
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. valerie.leger@pierroton.inra.fr.|University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France. valerie.leger@pierroton.inra.fr.
authors.forename: Valérie
authors.initials: V
authors.lastname: Léger
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France. joelle.amselem@versailles.inra.fr.
authors.forename: Joelle
authors.initials: J
authors.lastname: Amselem
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France. cbelser@genoscope.cns.fr.
authors.forename: Caroline
authors.initials: C
authors.lastname: Belser
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France. hadi.quesneville@versailles.inra.fr.
authors.forename: Hadi
authors.initials: H
authors.lastname: Quesneville
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Str 24, 3430, Tulln, Austria. Michael.Stierschneider@ait.ac.at.
authors.forename: Michael
authors.initials: M
authors.lastname: Stierschneider
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Str 24, 3430, Tulln, Austria. Silvia.Fluch@ait.ac.at.
authors.forename: Silvia
authors.initials: S
authors.lastname: Fluch
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany. lasse.feldhahn@ufz.de.
authors.forename: Lasse
authors.initials: L
authors.lastname: Feldhahn
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany. mika.tarkka@ufz.de.|iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany. mika.tarkka@ufz.de.
authors.forename: Mika
authors.initials: M
authors.lastname: Tarkka
authors.affiliation: iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany. sylvie.herrmann@ufz.de.|Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, 06120, Halle/Saale, Germany. sylvie.herrmann@ufz.de.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Herrmann
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany. francois.buscot@ufz.de.|iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany. francois.buscot@ufz.de.
authors.forename: François
authors.initials: F
authors.lastname: Buscot
authors.affiliation: Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France. Christophe.Klopp@toulouse.inra.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. antoine.kremer@pierroton.inra.fr.|University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France. antoine.kremer@pierroton.inra.fr.
authors.forename: Antoine
authors.initials: A
authors.lastname: Kremer
authors.affiliation: INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France. Jerome.SALSE@clermont.inra.fr.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Salse
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France. jmaury@genoscope.cns.fr.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France. plomion@pierroton.inra.fr.|University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France. plomion@pierroton.inra.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping; D018506:Gene Expression Regulation, Plant; D049810:Genetic Speciation; D018745:Genome, Plant; D057445:Plant Dormancy / Q000235:genetics*; D029963:Quercus / Q000235:genetics / Q000254:growth & development; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*