The pig X and Y sequencing project will produce high quality, finished sequences for both porcine sex chromosomes in an effort to facilitate a better understanding of their unique biology. In order to produce a comprehensive catalogue of all protein-coding, non-coding RNA and pseudogene loci, the Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute (WTSI) are undertaking full manual gene annotation of both sex chromosomes. This work will enhance our understanding of the gene content of these chromosomes, as well as allowing investigations of the patterns of X-Y homology and pig-specific testis-expressed genes not shared by other mammals. Additionally, the work will allow a comparison with the previously studied human and mouse sex chromosomes to provide further insight into the organisation and evolution of mammalian sex chromosomes.
There are currently 850 finished clones for pig chromosome X and assemblies for 898 draft clones for pig chromosome Y. ~50% of the chromosome X clones have been annotated which has currently yielded 388 protein-coding loci, 44 non-coding loci and 110 pseudogenes. All of the annotation will be made available through the Vertebrate Genome Annotation (VEGA) browser providing the user with a high quality reference gene set for the pig sex chromosomes, comparable to those already available in human and mouse. In addition a DAS source will be produced so users will be able to view the annotation alongside additional data in Ensembl.