Comparative Analysis of the Gene Sets of Mammalian Sex Chromosomes.

The recent sequencing and assembly of new versions of the porcine sex chromosomes at WTSI produced good quality reference genomic sequence highly suitable for the manual annotation approach employed by the Havana group at WTSI. We have produced full annotation for the pig X and Y chromosomes while updating our existing annotation for the human and mouse sex chromosomes in order to give us complete, up-to-date and consistent gene sets for all the sex chromosomes of these key mammalian species. Our annotation is notable for its high coverage of alternatively spliced transcripts, lncRNAs and pseudogene loci as well as detailed representation of functional potential at both gene and transcript levels. This unique data set has allowed us to conduct a comparative genomic analysis from key points across the mammalian lineage.

Here we present this comparative analysis, providing an investigation of the patterns of X-Y homology within the species and X-X/Y-Y between species. In addition we highlight the expansion of the C/T antigens on the human X chromosome and the massive duplication of HSFY-like loci on the pig Y chromosome as interesting case studies which allow us to further understand the evolution of the mammalian sex chromosomes.

All sequence and annotation data is available through the Vertebrate Genome Annotation (VEGA) browser (http://vega.sanger.ac.uk/), human and mouse GENCODE genesets via FTP (http://www.gencodegenes.org) and our annotation software is freely available via our website (http://www.sanger.ac.uk/resources/software/otterlace/).