title: Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis).
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada. jmm1@ualberta.ca.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Miller
authors.affiliation: Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, QLD, Australia. s.moore3@uq.edu.au.|Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada. s.moore3@uq.edu.au.
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Moore
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada. stothard@ualberta.ca.
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. liao_xp@tib.cas.cn.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Liao
authors.affiliation: Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada. david.coltman@ualberta.ca.
authors.forename: David W
authors.initials: DW
authors.lastname: Coltman
mesh_terms: D000818:Animals; D001483:Base Sequence; D055028:Comparative Genomic Hybridization; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D034581:Sheep, Bighorn / Q000235:genetics*; D034561:Sheep, Domestic / Q000235:genetics