A Contig Map of the Ovine Y Chromosome

The mammalian Y chromosome harbors genes essential for male reproduction and serves as a basis to understand chromosome evolution. The sheep is one of the major farmed animal species and is evolutionarily close to cattle. A high coverage sheep (ovine) genome assembly has been built. The ovine Y chromosome has not been included in this assembly due to highly repetitive sequences in the male-specific region (MSY). We report here the initial characterization of the ovine MSY (oMSY) by a combination of whole genome shotgun sequence (WGS) and BAC end sequence (BES). The WGS reads (~1 million pair-ends not assigned elsewhere in the genome assembly) were assembled into 4487 ovine Y-specific contigs (258 bp - 367 Kb) using a comparative assembly method based on the bovine MSY (bMSY) draft sequence. Alignment of the ovine BESs against the bMSY identified 605 Y chromosome BACs with one or both ends matched, of which 60 mapped in the X-degenerate and 545 in the ampliconic region. These BESs were used to orient the assembled contigs which resulted in a draft oMSY contig map that spans ~39 Mb (comparable to the 41.3 Mb of bMSY). The X-degenerate region contains genes well conserved with the bovine orthologs. The ampliconic region also contains a similar genetic composition to the bMSY, though its precise genomic organization requires further testing. This framework map of the oMSY, built with support from BESs and WGS assembly contigs, will be useful to study the genomic organization of the ovine Y chromosome.