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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 Laboratory

Title: Analysis of pig genomes provide insight into porcine demography and evolution)

Author
item Groenen, Martien
item Archibald, Alan
item Uenishi, Hirohide
item Tuggle, Christopher
item Takeuchi, Yasu
item Rothschild, Max
item Rogel-gaillard, Claire
item Park, Chankyu
item Milan, Denis
item Hendrik-jan, Megens
item Li, Shengting
item Larkin, Denis
item Kim, Heebal
item Franz, Laurent
item Caccamo, Mario
item Hyeonju, Ahn
item Aken, Bronwen
item Anselmo, Anna
item Anthon, Christian
item Auvil, Loretta
item Bouabid, Badaoui
item Beattie, Craig
item Bendixen, Christian
item Berman, Daniel
item Blecha, Frank
item Blomberg, Jonas
item Bolund, Lars
item Bosse, Mirte
item Botti, Sara
item Zhan, Bujie
item Bystrom, Megan
item Capitanu, Boris
item Silva, Denise
item Chardon, Patrick
item Chen, Celine
item Cheng, Ryan
item Choi, Sang-haeng
item Chow, William
item Clark, Richard
item Clee, Christopher
item Crooijmans, Richard
item Dawson, Harry
item Dehais, Patrice
item De sapio, Fiorabante
item Dibbits, Bert
item Drou, Nizar
item Du, Zhi-qiang
item Eversole, Kellye
item Fadista, Joao
item Fairley, Susan
item Faraut, Thomas
item Faulkner, Geoffrey
item Fowler, Katie
item Fredholm, Merete
item Fritz, Eric
item Gilbert, James
item Giuffra, Elisabetta
item Gorodkin, Jan
item Griffin, Darren
item Harrow, Jennifer
item Hayward, Alexander
item Howe, Kerstin
item Zhi-liang, Hu
item Humphray, Sean
item Hunt, Toby
item Hornshoj, Henrik
item Jeon, Jin-tae
item Jern, Patric
item Jones, Matthew
item Jurka, Jerzy
item Kanamori, Hiroyuki
item Kapetanovic, Ronan
item Jaebum, Kim
item Kim, Jae-hwan
item Kim, Kyu-won
item Kim, Tae-hun
item Larson, Greger
item Lee, Kyooyeol
item Lee, Kyung-tai
item Leggett, Richard
item Lewin, Harris
item Li, Yingrui
item Liu, Wansheng
item Loveland, Jane
item Lu, Yao
item Lunney, Joan
item Ma, Jian
item Madsen, Ole
item Mann, Katherine
item Mathews, Lucy
item Mclaren, Stuart
item Morozumi, Takeya
item Murtaug, Michael
item Narayan, Jitendra
item Nguyen, Dinh truong
item Ni, Peixiang
item Oh, Song-jung
item Onteru, Suneel
item Rohrer, Gary

Submitted to: Nature
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/27/2012
Publication Date: 11/15/2012
Publication URL: http://handle.nal.usda.gov/10113/56710
Citation: Groenen, M.A., Archibald, A.L., Uenishi, H., Tuggle, C., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Hendrik-Jan, M., Li, S., Larkin, D., Kim, H., Franz, L.A., Caccamo, M., Hyeonju, A., Aken, B.L., Anselmo, A., Anthon, C., Auvil, L., Bouabid, B., Beattie, C.W., Bendixen, C., Berman, D.J., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Zhan, B., Bystrom, M., Capitanu, B., Silva, D.C., Chardon, P., Chen, C.T., Cheng, R., Choi, S., Chow, W., Clark, R.C., Clee, C., Crooijmans, R.P., Dawson, H.D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G.J., Fowler, K.E., Fredholm, M., Fritz, E., Gilbert, J.G., Giuffra, E., Gorodkin, J., Griffin, D., Harrow, J.L., Hayward, A., Howe, K., Zhi-Liang, H., Humphray, S.J., Hunt, T., Hornshoj, H., Jeon, J., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Jaebum, K., Kim, J., Kim, K., Kim, T., Larson, G., Lee, K., Lee, K., Leggett, R., Lewin, H.A., Li, Y., Liu, W., Loveland, J.E., Lu, Y., Lunney, J.K., Ma, J., Madsen, O., Mann, K., Mathews, L., Mclaren, S., Morozumi, T., Murtaug, M.P., Narayan, J., Nguyen, D., Ni, P., Oh, S., Onteru, S., Rohrer, G.A., et al. 2012. Analysis of pig genomes provide insight into porcine demography and evolution. Nature. 491(7424):393-8.

Interpretive Summary: This manuscript describes the sequencing and analysis of the pig genome and its comparison with the genome of sequences of other wild and domestic pigs from Europe and Asia. Our efforts, as part of an international consortium, resulted in the manual annotation of over 1,400 genes to provide a basic description of the pig immunome i.e., the portion of the genome devoted to the immune response. We also conducted a large-scale comparative assessment of the pig, mouse, bovine and human genomes focusing on shared and unique gene families involved in immunity and inflammation. This analysis revealed an overwhelming similarity of pigs to humans compared to mice and cows for most parameters evaluated thus validating their use as a useful biomedical model. It also identified cow and pig-specific expansion of certain gene families. These efforts will contribute significantly toward promoting human and swine health.

Technical Abstract: For nearly 8,000 years pigs and humans have shared a close and complex relationship, and through domestication and breeding, humans have shaped the genomes of current diverse pig breeds. Here we present the assembly and analysis of the genome sequence of a female domestic pig from the European Duroc breed and its comparison with the genome of sequences of other wild and domestic pigs from Europe and Asia. Pigs (Sus scrofa) emerged in Southeast Asia and subsequently spread across most of Eurasia. Our sequence results show a deep phylogenetic split between European and Asian wild boars that occurred around 1 million years ago. We identified fixed differences at over 1,700 amino- acids positions in almost 1,200 different genes and a selective sweep analysis indicated strong selection on genes involved in RNA processing and regulation. A comparison with other mammals demonstrated the rapid evolution of immune related and olfactory receptor encoding genes. Rapid gene expansions were observed for the cathelicidin, type I interferon and olfactory gene families. Pig, together with the rat, has the largest repertoire of functional olfactory receptor genes seen in any other species reflecting the importance of smell in this scavenging animal. For millennia the pig has served as an important source for animal protein for human nutrition, but more recently because of its similar physiology to humans, it has also become an important biomedical animal model. The pig genome sequence provides an important resource for further improvements of this important livestock species and our identification of many putative disease-causing variants in the porcine genome extends the potential of the pig as a biomedical model. Supported by funds from ARS Project Plans 1235-51000-055-00D and 1265-32000-098-00D and BARC summer student fellowships.

Last Modified: 8/24/2016
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