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

BMC Genomics
Isabelle LesurChristophe Plomion

Abstract

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 ...Continue Reading

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May 7, 2015·Molecular Ecology Resources·Christophe PlomionAntoine Kremer
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Datasets Mentioned

BETA
AT3G04920

Methods Mentioned

BETA
RNAseq
454 sequencing
PCR
RNA-seq

Software Mentioned

Diginorm
Phred
Pathway Studio
blastall
MIRA
CAP3
R statistics
BlastX
kmer
ClustalW

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