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

Lesur Isabelle, Le Provost Grégoire, Bento Pascal, Da Silva Corinne, Leplé Jean-Charles, Murat Florent, Ueno Saneyoshi, Bartholomé Jérôme, Lalanne Céline, Ehrenmann François, Noirot Céline, Burban Benoit, Léger Valérie, Amselem Joelle, Belser Caroline, Quesneville Hadi, Stierschneider Michael, Fluch Silvia, Feldhahn Lasse, Tarkka Mika, Herrmann Sylvie, Buscot François, Klopp Christophe, Kremer Antoine, Salse Jérôme, Aury Jean-Marc, Plomion Christophe. 2015. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics, 16:112, 23 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
Published version - Anglais
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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.

Mots-clés Agrovoc : Quercus robur, Quercus petraea, Expression des gènes, Séquence d'ARN, genomic features [EN], Bourgeon, Phénologie, Génotype, Phénotype, Transcription génique, Fagaceae

Classification Agris : K01 - Forestry - General aspects
F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Lesur Isabelle, INRA (FRA)
  • Le Provost Grégoire, INRA (FRA)
  • Bento Pascal, CEA (FRA)
  • Da Silva Corinne, CEA (FRA)
  • Leplé Jean-Charles, INRA (FRA)
  • Murat Florent, INRA (FRA)
  • Ueno Saneyoshi, Forestry and Forest Products Research Institute (JPN)
  • Bartholomé Jérôme, INRA (FRA) ORCID: 0000-0002-0855-3828
  • Lalanne Céline, INRA (FRA)
  • Ehrenmann François, INRA (FRA)
  • Noirot Céline, INRA (FRA)
  • Burban Benoit, INRA (FRA)
  • Léger Valérie, INRA (FRA)
  • Amselem Joelle, INRA (FRA)
  • Belser Caroline, CEA (FRA)
  • Quesneville Hadi, INRA (FRA)
  • Stierschneider Michael, AIT [Austriche] (AUT)
  • Fluch Silvia, AIT [Austriche] (AUT)
  • Feldhahn Lasse, Helmholtz Centre for Environmental Research (DEU)
  • Tarkka Mika, Helmholtz Centre for Environmental Research (DEU)
  • Herrmann Sylvie, iDiv (DEU)
  • Buscot François, Helmholtz Centre for Environmental Research (DEU)
  • Klopp Christophe, INRA (FRA)
  • Kremer Antoine, INRA (FRA)
  • Salse Jérôme, INRA (FRA)
  • Aury Jean-Marc, CEA (FRA)
  • Plomion Christophe, INRA (FRA) - auteur correspondant

Source : Cirad-Agritrop (

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