Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)

BMC Genomics

David W Coltman²  Xiaoping Liao³  Paul Stothard¹  Stephen S Moore¹  Joshua M Miller² 

[1] Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada;Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada;Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China

关键词: Domestication;    Comparative genomics;    Cross-species alignment;   

Others  :  1203910
DOI  :  10.1186/s12864-015-1618-x

 received in 2015-01-12, accepted in 2015-05-05,  发布年份 2015

【 摘 要 】

Background

Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries).

Results

Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition.

Conclusion

Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics.

【 授权许可】

   
2015 Miller et al.; licensee BioMed Central.

【 图 表 】

Fig. 1.

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