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

• DOI: 10.1186/s12864-015-1331-9
• Publication Date: 2015-02-20T06:37:57Z
• Authors: Isabelle Lesur; Grégoire Le Provost; Pascal Bento; Corinne Da Silva; Jean-Charles Leplé; Florent Murat; Saneyoshi Ueno; Jerôme Bartholomé; Céline Lalanne; François Ehrenmann; Céline Noirot; Christian Burban; Valérie Léger; Joelle Amselem; Caroline Belser; Hadi Quesneville; Michael Stierschn...; Silvia Fluch; Lasse Feldhahn; Mika Tarkka; Sylvie Herrmann; François Buscot; Christophe Klopp; Antoine Kremer; Jérôme Salse; Jean-Marc Aury; Christophe Plomion
• Keywords: 0301 basic medicine; [SDV]Life Sciences [q-bio]; comparative genomics; Fagaceae; F30 - Génétique et amélioration des plantes; Quercus; bud phenology; Gene Expression Regulation, Plant; K01 - Foresterie - Considérations générales; http://aims.fao.org/aos/agrovoc/c_3225; http://aims.fao.org/aos/agrovoc/c_2773; bourgeon; Chromosome Mapping; Plant Dormancy; Adaptation, Physiological; phénologie; phénotype; http://aims.fao.org/aos/agrovoc/c_35128; quercus; génotype; Quercus robur; Genome, Plant; expression des gènes; Biotechnology; Research Article; 570; caractéristique génomique; Genetic Speciation; Quercus petraea; fagaceae; de novo assembly; http://aims.fao.org/aos/agrovoc/c_27813; 03 medical and health sciences; oak; séquençage; Genetics; oak;transcriptome;de novo assembly;comparative genomics;RNA-seq;bud phenology; 580; Base Sequence; Transcription génique; génomique comparative; Sequence Analysis, RNA; http://aims.fao.org/aos/agrovoc/c_24692; http://aims.fao.org/aos/agrovoc/c_331060; 15. Life on land; http://aims.fao.org/aos/agrovoc/c_27527; dormance; http://aims.fao.org/aos/agrovoc/c_5774; http://aims.fao.org/aos/agrovoc/c_15794; http://aims.fao.org/aos/agrovoc/c_5776; séquence d'arn; http://aims.fao.org/aos/agrovoc/c_1135; RNA-seq; Transcriptome; transcriptome

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.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.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.