The Sheep Genome(s), From Reference To Variome

Version 3.1 of the sheep reference genome (Ovis aries, breed Texel) has been deposited in GenBank. The assembly has a total length of 2.6Gb with a contig N50 of 40kb and contains 84Mb of gaps. 3,381 scaffolds (N50 100Mb) have been assigned to chromosomes. To facilitate annotation by ENSEMBL the next full reassembly will not be released until mid 2014. The detailed comparison of the sheep assembly with the bovine genome assemblies has identified ~145 regions with more than a 200 kb differences between the two genomes. 46 are on the X chromosome. Excluding the X chromosome 19 have been identified as true species differences, whilst many of the 29 regions involving assembly issues in the sheep genome are associated with multi- copy gene families. High quality assemblies of these regions will be a key focus of the reference genome project over the next eighteen months. Update patches will be released as the regional assemblies are completed.

To initiate the development of a catalogue of the O. aries variome, ~10 X mapped read coverage was generated from each of 68 diverse domestic sheep , 3 Ovis canadensis (bighorn) and 2 Ovis dalli (thinhorn) individuals. The Illumina reads from each animal were aligned to the reference genome to identify SNPs and indels. The dataset is being used to identify signatures associated with domestication and the selection for desirable wool and meat characteristics. By comparing with the variomes of ruminant species a picture of the evolution of the ruminant clade is emerging.