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Title: Structural and Functional Annotation of the Porcine Immunome

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

Submitted to: Biomed Central (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.