Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks.

ABSTRACT:

Background

Reference transcriptomes provide valuable resources for understanding evolution within and among species. We de novo assembled and annotated a reference transcriptome for Quercus lobata and Q. garryana and identified single-nucleotide polymorphisms (SNPs) to provide resources for forest genomicists studying this ecologically and economically important genus. We further performed preliminary analyses of genes important in interspecific divergent (positive) selection that might explain ecological differences among species, estimating rates of nonsynonymous to synonymous substitutions (d N/d S) and Fay and Wu's H. Functional classes of genes were tested for unusually high d N/d S or low H consistent with divergent positive selection.

Results

Our draft transcriptome i

SUBMITTER: Cokus SJ 

PROVIDER: S-EPMC4517385 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature