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

BMC Genomics

Victoria L. Sork¹  Paul F. Gugger²  Shawn J. Cokus³ 

[1] Institute of the Environment and Sustainability, University of California, 300 La Kretz Hall, 619 Charles E. Young Drive East, Los Angeles 90095-1496, CA, USA;Ecology and Evolutionary Biology, University of California, 4140 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles 90095-7239, CA, USA;Molecular, Cell, and Developmental Biology, University of California, 3000 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles 90095-7239, CA, USA

关键词: Transcriptome;    Single-nucleotide polymorphism;    RNA-Seq;    Quercus lobata;    Quercus garryana;    Quercus douglasii;    d N/d S;    Divergence;    De novo assembly;    Annotation;   

Others  :  1221852
DOI  :  10.1186/s12864-015-1761-4

 received in 2014-11-10, accepted in 2015-07-07,  发布年份 2015

【 摘 要 】

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_Sor low H consistent with divergent positive selection.

Results

Our draft transcriptome is among the most complete for oaks, including 83,644 contigs (23,329 ≥ 1 kbp), 14,898 complete and 13,778 partial gene models, and functional annotations for 9,431 Arabidopsis orthologs and 19,365 contigs with Pfam hits. We identified 1.7 million possible sequence variants including 1.1 million high-quality diallelic SNPs — among the largest sets identified in any tree. 11 of 18 functional categories with significantly elevated d_N /d_Sare involved in disease response, including 50+ genes with d_N /d_S  > 1. Other high-d_N /d_Sgenes are involved in biotic response, flowering and growth, or regulatory processes. In contrast, median d_N /d_Swas low (0.22), suggesting that purifying selection influences most genes. No functional categories have unusually low H.

Conclusions

These results offer preliminary support for the hypothesis that divergent selection at pathogen resistance are important factors in species divergence in these hybridizing California oaks. Our transcriptome provides a solid foundation for future studies of gene expression, natural selection, and speciation in Quercus.

【 授权许可】

   
2015 Cokus et al.

【 图 表 】

Fig. 1.

Fig. 2.

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