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.
Highlights
Many northern-hemisphere forests are dominated by oaks
By studying the dynamics of gene expression over this critical period, focusing on two successive phases of bud dormancy release: i) ecodormancy, a dormancy state prevailing in late winter and spring imposed by environmental conditions unfavorable for growth, and ii) swelling bud, which occurs in spring, just before bud burst, when the heat requirement for bud break is almost satisfied
The main objectives of this study were: i) to enlarge the current oak expressed sequence tags (ESTs) resource through the use of ultrahighthroughput sequencing technology and to combine the data obtained with available sequences expressed in different tissues, at different developmental stages, and in response to different biotic and abiotic stresses, to generate the most comprehensive annotated unigene set for oak, and ii) to use this resource to increase our understanding of the structure, function and macroevolution of the oak genome
Summary
Many northern-hemisphere forests are dominated by oaks These species extend over diverse environmental conditions and are interesting models for studies of plant adaptation and speciation. The effect of climate change, with milder autumns and warmer winters, on the timing of bud flush and the impact of exposure to late spring frost are key questions in forestry requiring a detailed understanding of the physiological and molecular mechanisms (and their genetic variability) involved in dormancy release We addressed these questions, by studying the dynamics of gene expression over this critical period, focusing on two successive phases of bud dormancy release: i) ecodormancy, a dormancy state prevailing in late winter and spring imposed by environmental conditions unfavorable for growth (i.e. heat requirement not fulfilled), and ii) swelling bud, which occurs in spring, just before bud burst, when the heat requirement for bud break is almost satisfied
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