Page Banner

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 Laboratory

Title: Structural and Functional Annotation of the Porcine Immunome)

Author
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: 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.

Last Modified: 8/24/2016
Footer Content Back to Top of Page