Structural and Functional Annotation of the Porcine Immunome

Authors: Dawson, Harry; LOVELAND, JANE - Wellcome Trust Sanger Institute; PASCAL, GERALDINE - Institut National De La Recherche Agronomique (INRA); GILBERT, JAMES - Wellcome Trust Sanger Institute; UENISHI, HIROHIDI - National Institute Of Agrobiological Sciences (NIAS); Mann, Katherine; SANG, YONG-MING - Arkansas State University; ZHANG, JIE - Huazhong Agricultural University; CARVALHO-SILVA, DENISE - European Bioinformatics Institute; HUNT, TOBY - Wellcome Trust Sanger Institute; HARDY, MATHEW - Wellcome Trust Sanger Institute; HU, ZHILIANG - Iowa State University; ZHAO, SHU-HONG - Huazhong Agricultural University; ANSELMO, ANNA - Parco Tecnologico Padano; SINKAI, HIROKI - National Institute Of Agrobiological Sciences (NIAS); Chen, Celine; BADAOUI, BOUABID - Parco Tecnologico Padano; Berman, Daniel; AMID, CLARA - Wellcome Trust Sanger Institute; KAY, MIKE - Wellcome Trust Sanger Institute; LLOYD, DAVID - Wellcome Trust Sanger Institute; SNOW, CATHERINE - Wellcome Trust Sanger Institute; MOROZUMI, TAKEYA - Institute Of Japan Association For Technology In Agriculture, Forestry And Fisheries; CHENG, RYAN PEI-YEN - Iowa State University; BYSTROM, MEGAN - Iowa State University; BOURNEUF, EMMANUELLE - Institut National De La Recherche Agronomique (INRA); KAPETANOVIC, RONAN - University Of Edinburgh; SCHWARTZ, JOHN - University Of Minnesota; KATARIA, RAIJIT - National Bureau Of Plant Genetic Resources; ASTLEY, MATTHEW - Wellcome Trust Sanger Institute; FRITZ, ERIC - Iowa State University; STEWARD, CHARLES - Wellcome Trust Sanger Institute; THOMAS, MARK - Wellcome Trust Sanger Institute; WILMING, LAURENS - Wellcome Trust Sanger Institute; GIUFFRA, ELISABETTA - Institut National De La Recherche Agronomique (INRA); ARCHIBALD, ALAN - University Of Edinburgh; BED'HOM, BERTRAND - Institut National De La Recherche Agronomique (INRA); BERALDI, DARIO - University Of Edinburgh; AIT-ALI, TAHAR - University Of Edinburgh; BLECHA, FRANK - Kansas State University; BOTTI, SARA - Parco Tecnologico Padano; FREEMAN, TOM - University Of Edinburgh; HUME, DAVID - University Of Edinburgh; Lunney, Joan; MURTAUGH, MICHAEL - University Of Minnesota; REECY, JAMES - Iowa State University; HARROW, JENNIFER - Wellcome Trust Sanger Institute; ROGEL-GAILLARD, CLAIRE - Institut National De La Recherche Agronomique (INRA); TUGGLE, CHRISTOPHER - Iowa State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/3/2013
Publication Date: 5/15/2013
Publication URL: http://handle.nal.usda.gov/10113/56718
Citation: Dawson, H.D., Loveland, J., Pascal, G., Gilbert, J., Uenishi, H., Mann, K., Sang, Y., Zhang, J., Carvalho-Silva, D., Hunt, T., Hardy, M., Hu, Z., Zhao, S., Anselmo, A., Sinkai, H., Chen, C.T., Badaoui, B., Berman, D.J., Amid, C., Kay, M., Lloyd, D., Snow, C., Morozumi, T., Cheng, R., Bystrom, M., Bourneuf, E., Kapetanovic, R., Schwartz, J.C., Kataria, R., Astley, M., Fritz, E., Steward, C., Thomas, M., Wilming, L., Giuffra, E., Archibald, A., Bed'Hom, B., Beraldi, D., Ait-Ali, T., Blecha, F., Botti, S., Freeman, T., Hume, D.A., Lunney, J.K., Murtaugh, M.P., Reecy, J.M., Harrow, J., Rogel-Gaillard, C., Tuggle, C.K. 2013. Structural and Functional Annotation of the Porcine Immunome. Biomed Central (BMC) Genomics. 14:332-370.

Interpretive Summary: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immune response, or its immunome, are not well-characterized. However, the completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems. To accomplish this, the Immune Response Annotation Group (IRAG) used computational curation and manual annotation to define 1,369 immunity-related genes through sequence-based comparison to genes in other species. This analysis defines a core gene set for the pig immunome and adds significantly to porcine immune response gene annotations. A four species comparison (human, mouse, cow, pig) revealed that humans and pigs have far less gene duplication and more gene conservation than do humans and mice, or humans and cows.This reinforces the importance and utility of the pig as a species to model the immune response of humans. These results will also be used by animal health professionals to understand pig immune responses to infection and help develop better vaccines and therapeutics for treating pig diseases and modeling human disease responses.

Technical Abstract: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. However, the completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems. The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Global gene expression data were also used to identify both shared and species-specific immune responses. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 non-organism-supported transcripts were also detected. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations provided evidence for co-expression of the IRAG genes and many un-annotated porcine genes. This analysis defines a core gene set for the pig immunome and adds significantly to porcine immune response gene annotations. In addition, among all available proteins encoded by genes in the core immunome cluster, 15% showed an accelerated evolution as compared to 4.1% across the entire genome. This result confirms immune functions represent major targets in pig evolution, as in other species.