Structural and functional annotation of the porcine immunome

Dawson, Harry D., Loveland, Jane E., Pascal, Geraldine, Gilbert, James G. R., Uenishi, Hirohide, Mann, Katherine M., Sang, Yongming, Zhang, Jie, Carvalho-Silva, Denise, Hunt, Toby, Hardy, Matthew, Hu, Zhiliang, Zhao, Shu-Hong, Anselmo, Anna, Shinkai, Hiroki, Chen, Celine, Badaoui, Bouabid, Berman, Daniel, Amid, Clara, Kay, Mike, Lloyd, David, Snow, Catherine, Morozumi, T., Cheng, Ryan Pei-Yen, Bystrom, Megan, Kapetanovic, Ronan, Schwartz, John C., Kataria, Ranjit, Astley, Matthew, Fritz, Eric, Steward, Charles, Thomas, Mark, Wilming, Laurens, Toki, Daisuke, Archibald, Alan L., Bed'Hom, Bertrand, Beraldi, Dario, Huang, Ting-Hua, Ait-Ali, Tahar, Blecha, Frank, Botti, Sara, Freeman, Tom C., Giuffra, Elisabetta, Hume, David A., Lunney, Joan K., Murtaugh, Michael P., Reecy, James M., Harrow, Jennifer L., Rogel-Gaillard, Claire and Tuggle, Christopher K. (2013) Structural and functional annotation of the porcine immunome. BMC Genomics, 14 1: 332.1-332.16. doi:10.1186/1471-2164-14-332

Author Dawson, Harry D.
Loveland, Jane E.
Pascal, Geraldine
Gilbert, James G. R.
Uenishi, Hirohide
Mann, Katherine M.
Sang, Yongming
Zhang, Jie
Carvalho-Silva, Denise
Hunt, Toby
Hardy, Matthew
Hu, Zhiliang
Zhao, Shu-Hong
Anselmo, Anna
Shinkai, Hiroki
Chen, Celine
Badaoui, Bouabid
Berman, Daniel
Amid, Clara
Kay, Mike
Lloyd, David
Snow, Catherine
Morozumi, T.
Cheng, Ryan Pei-Yen
Bystrom, Megan
Kapetanovic, Ronan
Schwartz, John C.
Kataria, Ranjit
Astley, Matthew
Fritz, Eric
Steward, Charles
Thomas, Mark
Wilming, Laurens
Toki, Daisuke
Archibald, Alan L.
Bed'Hom, Bertrand
Beraldi, Dario
Huang, Ting-Hua
Ait-Ali, Tahar
Blecha, Frank
Botti, Sara
Freeman, Tom C.
Giuffra, Elisabetta
Hume, David A.
Lunney, Joan K.
Murtaugh, Michael P.
Reecy, James M.
Harrow, Jennifer L.
Rogel-Gaillard, Claire
Tuggle, Christopher K.
Title Structural and functional annotation of the porcine immunome
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2013-05-15
Year available 2013
Sub-type Article (original research)
DOI 10.1186/1471-2164-14-332
Open Access Status DOI
Volume 14
Issue 1
Start page 332.1
End page 332.16
Total pages 16
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Subject 1305 Biotechnology
1311 Genetics
Formatted abstract
Background: 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. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems.

Results: 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. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome.

Conclusions: This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig's adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response.
Keyword Accelerated evolution
Co expression network
Genome annotation
Immune response
Phylogenetic analysis
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID P20-RR017686
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 58 times in Thomson Reuters Web of Science Article | Citations
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Created: Fri, 16 May 2014, 21:43:45 EST by Ronan Kapetanovic on behalf of Institute for Molecular Bioscience