Structural and functional annotation of immunity-related genes in the pig genome

The structure and function of the porcine immunome is poorly characterized. The main purpose of the Immune Response Annotation Group (IRAG) is to use computational and manual curation to refine the currently available automated annotation of immunity-related genes through sequence-based comparison to such genes in other species. Transcriptomic data are also being used to confirm the involvement of these genes in immune response. A gene list was compiled using gene ontology annotation and literature sources, and sequence data and annotation information were used to find candidate genome regions for annotation. Manual annotation for ~1,500 loci has been completed by group members using genome sequence assembly 9 (Sscrofa9) and WTSI Otterlace/Zmap software, which provides alignments of genomic contigs with public sequence data. These alignments are analyzed to confirm/extend exon-intron boundaries, propose new alternative splice products, and improve protein sequence predictions. Over 1,100 transcripts (>30%) were annotated using only non-porcine sequences. Preliminary results show evidence for at least eight gene duplications and many new alternative splice variants. Over 50 immune genes were not found. All results will be checked against assembly 10 (Sscrofa10); initial results for 749 IRAG genes with RNA data shows 7.9% are absent in Sscrofa10. A correlation-based network analysis of transcriptomic data from experimental infections or immune stimulations provided evidence for involvement of the IRAG gene set in immune response and identified putative new immune response genes. Our future challenge will be to identify the underlying biology specific to the pig species from this major annotation effort.