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

摘要: Reference transcriptomes provide valuable resources for understanding evolution within and among species. We de novo assembled annotated a reference transcriptome Quercus lobata Q. garryana identified single-nucleotide polymorphisms (SNPs) to forest genomicists studying this ecologically economically important genus. further performed preliminary analyses of genes in interspecific divergent (positive) selection that might explain ecological differences species, estimating rates nonsynonymous synonymous substitutions (d N/d S) Fay Wu’s H. Functional classes were tested unusually high d S or low H consistent with positive selection. Our draft is the most complete oaks, including 83,644 contigs (23,329 ≥ 1 kbp), 14,898 13,778 partial gene models, functional annotations 9,431 Arabidopsis orthologs 19,365 Pfam hits. 1.7 million possible sequence variants 1.1 high-quality diallelic SNPs — largest sets any tree. 11 18 categories significantly elevated are involved disease response, 50+ S > 1. Other high-d biotic flowering growth, regulatory processes. In contrast, median was (0.22), suggesting purifying influences genes. No have These results offer support hypothesis at pathogen resistance factors species divergence these hybridizing California oaks. provides solid foundation future studies expression, natural selection, speciation Quercus.