Structural and functional annotation of the porcine immunome

BMC Genomics

Research Article

Frank Blecha¹  Yongming Sang¹  James M Reecy²  Megan Bystrom²  Ryan Pei-Yen Cheng²  Ting-Hua Huang²  Eric Fritz²  Zhiliang Hu²  Christopher K Tuggle²  John C Schwartz³  Michael P Murtaugh³  Bertrand Bed’Hom⁴  Claire Rogel-Gaillard⁴  Géraldine Pascal⁵  Mark Thomas⁶  Matthew Astley⁶  David Lloyd⁶  Charles Steward⁶  Catherine Snow⁶  James GR Gilbert⁶  Mike Kay⁶  Matthew Hardy⁶  Jennifer L Harrow⁶  Jane E Loveland⁶  Toby Hunt⁶  Laurens Wilming⁶  Denise Carvalho-Silva⁷  Clara Amid⁷  Takeya Morozumi⁸  Daisuke Toki⁸  Shu-Hong Zhao⁹  Jie Zhang⁹  Ranjit Kataria^1,10  Hiroki Shinkai^1,11  Hirohide Uenishi^1,11  Sara Botti^1,12  Bouabid Badaoui^1,12  Anna Anselmo^1,12  Elisabetta Giuffra^1,13  Alan L Archibald^1,14  Ronan Kapetanovic^1,14  Tom C Freeman^1,14  Dario Beraldi^1,14  David A Hume^1,14  Tahar Ait-Ali^1,14  Katherine M Mann^1,15  Joan K Lunney^1,15  Daniel Berman^1,15  Celine Chen^1,16  Harry D Dawson^1,16 

[1] Department of Anatomy and Physiology, College of Veterinary Medicine, 66506, Manhattan, KS, USA;Department of Animal Science, Iowa State University, 50011, Ames, IA, USA;Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, 55108, St. Paul, MN, USA;INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350, Jouy-en-Josas, France;INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France;Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA, Hinxton, Cambs, UK;Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA, Hinxton, Cambs, UK;Current affiliation: EMBL Outstation-Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambs, UK;Institute of Japan Association for Technology in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan;Laboratory of Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, 430070, Wuhan, PR China;National Bureau of Animal Genetic Resources, P.B. 129, GT Road By-Pass, 132001, Karnal, Haryana, India;National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan;Parco Tecnologico Padano, Integrative Biology Unit, via A. Einstein, 26900, Lodi, Italy;Parco Tecnologico Padano, Integrative Biology Unit, via A. Einstein, 26900, Lodi, Italy;INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350, Jouy-en-Josas, France;The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Easter Bush, Midlothian, UK;USDA ARS BA Animal Parasitic Diseases Laboratory, 20705, Beltsville, MD, USA;USDA-ARS, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, 20705, Beltsville, MD, USA;

关键词: Immune response;    Porcine;    Genome annotation;    Co-expression network;    Phylogenetic analysis;    Accelerated evolution;   

DOI  :  10.1186/1471-2164-14-332

 received in 2013-03-02, accepted in 2013-05-03,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsThe 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© Dawson et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.