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

Abstract

BackgroundMany 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.ResultsThe 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.ConclusionIn 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 materialThe online version of this article (doi:10.1186/s12864-015-1331-9) contains supplementary material, which is available to authorized users.

Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting

“…Recently, an oak gene expression atlas was also generated for two sympatric oak species, Quercus robur (pedunculated oak) and Quercus petraea [9], which identified genes associated with vegetative bud phenology and contributed relevant information for the annotation of the pedunculated oak's genome. The gene expression studies performed in cork oak have mainly targeted the identification of genes involved in cork formation, and several candidate genes have been revealed [10].…”

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

“…(Lesur et al 2015), and the quality and availability of P. persica genome annotation (Verde et al 2013(Verde et al , 2017.…”

“…BlastN best hits for our working assembly (orict) original contigs and for the amplified expected fragments (orict-cut) were first retrieved using Lesur et al (2015)" most recent oak assembly (ocv4, see Table S2-C, Supporting information). Consensus of candidate regions originated from both orict and ocv4 (396 and 368 respectively, see Table S2-A, S2-B, and Appendix S1, Supporting information), aiming at retrieving the longest consensus sequences that included the resequenced gene regions, while avoiding to target those with possible chimeric sequences likely different to the regions being successfully resequenced.…”

“…In Fagaceae, previous comparative mapping and "omics" technologies (reviewed in Kremer et al 2012) with recent development of genomic resources (e.g. FaivreRampant et al 2011;Tarkka et al 2013;Lesur et al 2015;Lepoittevin et al 2015, Bodénès et al 2016 set the path to very recent release of genome sequences to the research community (Quercus lobata, Sork et al 2016;Q. robur, Plomion et al 2016Q.…”

“…To that end, we validated previous unpublished Sanger sequence data for fragments of targeted gene regions in a panel of individuals sampled across a large part of both species geographic range. Both functional and expressional candidate genes potentially involved in species ecological preferences, phenology and host-pathogen interactions were targeted, as well as a reference set of fragments randomly chosen across the last oak unigene (Lesur et al 2015). These data were obtained within the framework of the EVOLTREE network activities (http://www.evoltree.eu/).…”