Adding Value To The Pig Genome Sequence

A high quality annotated reference genome sequence is critical to contemporary biological research. The Swine Genome Sequencing Consortium have recently published a draft reference pig genome (Groenen et al 2012 Nature Nature 491: 393-8). However, establishing its sequence is only the first step in characterizing a genome. Identifying the functional elements within the genome sequence is essential for understanding the phenotypic consequences encoded in the genome. The annotation of the pig genome sequence is currently limited to gene models deduced from alignments with expressed sequences (cDNA, ESTs, RNaseq) and some sequence variation (SNPs). Whilst the publication of a draft genome sequence represents an important achievement and milestone for the pig genetics and genomics research community the value of the genome sequence could be enhanced through further research and analysis. First, the BAC clone based framework of the reference genome provides a template for locus-specific improvement of the reference sequence. Second, the sequencing of multiple individual pigs reveals the extent of genetic variation in pigs at nucleotide resolution. Third, next-generation sequencing technologies have transformed the ease with which functional DNA elements can be identified on a genome-wide scale and dramatically reduced the costs of such experiments. By focusing on a subset of assays - RNAseq, Transcription Start Sites (CAGE), histone marks and methylation states - and by coordinating efforts to minimise redundant activity it should be possible to make significant progress towards enhanced annotation analogous to the outputs from the ENCODE consortium. I will describe how these objectives could be achieved in part through community based efforts and the work of the Ensembl team to make the enhanced annotation accessible.