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United States Department of Agriculture

Agricultural Research Service

Research Project: DIET AND IMMUNE FUNCTION RELATED TO INFECTIOUS AND ALLERGIC DISEASE

Location: Diet, Genomics and Immunology Lab

Title: Structural and Functional Annotation of the Porcine Immunome

Authors
item Dawson, Harry
item Loveland, Jane -
item Pascal, Geraldine -
item Gilbert, James -
item Uenishi, Hirohidi -
item Mann, Katherine
item Sang, Yong-Ming -
item Zhang, Jie -
item Carvalho-Silva, Denise -
item Hunt, Toby -
item Hardy, Mathew -
item Hu, Zhiliang -
item Zhao, Shu-Hong -
item Anselmo, Anna -
item Sinkai, Hiroki -
item Chen, Celine
item Badaoui, Bouabid -
item Berman, Daniel
item Amid, Clara -
item Kay, Mike -
item Lloyd, David -
item Snow, Catherine -
item Morozumi, Takeya -
item Cheng, Ryan Pei-Yen -
item Bystrom, Megan -
item Bourneuf, Emmanuelle -
item Kapetanovic, Ronan -
item Schwartz, John -
item Kataria, Raijit -
item Astley, Matthew -
item Fritz, Eric -
item Steward, Charles -
item Thomas, Mark -
item Wilming, Laurens -
item Giuffra, Elisabetta -
item Archibald, Alan -
item Bed'hom, Bertrand -
item Beraldi, Dario -
item Ait-Ali, Tahar -
item Blecha, Frank -
item Botti, Sara -
item Freeman, Tom -
item Hume, David -
item Lunney, Joan
item Murtaugh, Michael -
item Reecy, James -
item Harrow, Jennifer -
item Rogel-Gaillard, Claire -
item Tuggle, Christopher -

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 3, 2013
Publication Date: May 15, 2013
Repository 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.

Last Modified: 9/21/2014