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

Author
item GROENEN, MARTIEN - Wageningen University
item ARCHIBALD, ALAN - University Of Edinburgh
item UENISHI, HIROHIDE - National Institute Of Agrobiological Sciences (NIAS)
item TUGGLE, CHRISTOPHER - Iowa State University
item TAKEUCHI, YASU - University College London
item ROTHSCHILD, MAX - Iowa State University
item ROGEL-GAILLARD, CLAIRE - Institut National De La Recherche Agronomique (INRA)
item PARK, CHANKYU - Konkuk University
item MILAN, DENIS - Institut National De La Recherche Agronomique (INRA)
item HENDRIK-JAN, MEGENS - Wageningen University
item LI, SHENGTING - Aarhus University
item LARKIN, DENIS - Aberystwyth University
item KIM, HEEBAL - Seoul National University
item FRANZ, LAURENT - Wageningen University
item CACCAMO, MARIO - The Genome Analysis Centre
item HYEONJU, AHN - Seoul National University
item AKEN, BRONWEN - Wellcome Trust Sanger Institute
item ANSELMO, ANNA - Parco Tecnologico Padano
item ANTHON, CHRISTIAN - University Of Copenhagen
item AUVIL, LORETTA - University Of Illinois
item BOUABID, BADAOUI - Parco Tecnologico Padano
item BEATTIE, CRAIG - University Of Illinois
item BENDIXEN, CHRISTIAN - Aarhus University
item Berman, Daniel
item BLECHA, FRANK - Arkansas State University
item BLOMBERG, JONAS - Uppsala University
item BOLUND, LARS - Aarhus University
item BOSSE, MIRTE - University Of Edinburgh
item BOTTI, SARA - Parco Tecnologico Padano
item ZHAN, BUJIE - Aarhus University
item BYSTROM, MEGAN - Iowa State University
item CAPITANU, BORIS - University Of Illinois
item SILVA, DENISE - Wellcome Trust Sanger Institute
item CHARDON, PATRICK - Institut National De La Recherche Agronomique (INRA)
item Chen, Celine
item CHENG, RYAN - Iowa State University
item CHOI, SANG-HAENG - Korean Bioinformation Center (KOBIC)
item CHOW, WILLIAM - Wellcome Trust Sanger Institute
item CLARK, RICHARD - Wellcome Trust Sanger Institute
item CLEE, CHRISTOPHER - Wellcome Trust Sanger Institute
item CROOIJMANS, RICHARD - Wageningen University
item Dawson, Harry
item DEHAIS, PATRICE - Inland Northwest Research Alliance, Inra
item DE SAPIO, FIORABANTE - University Of Edinburgh
item DIBBITS, BERT - Wageningen University
item DROU, NIZAR - University Of Edinburgh
item DU, ZHI-QIANG - Iowa State University
item EVERSOLE, KELLYE - Eversole Associates
item FADISTA, JOAO - Aarhus University
item FAIRLEY, SUSAN - Parco Tecnologico Padano
item FARAUT, THOMAS - Institut National De La Recherche Agronomique (INRA)
item FAULKNER, GEOFFREY - University Of Edinburgh
item FOWLER, KATIE - University Of Kent
item FREDHOLM, MERETE - University Of Copenhagen
item FRITZ, ERIC - Iowa State University
item GILBERT, JAMES - Wellcome Trust Sanger Institute
item GIUFFRA, ELISABETTA - Institut National De La Recherche Agronomique (INRA)
item GORODKIN, JAN - University Of Copenhagen
item GRIFFIN, DARREN - University Of Kent
item HARROW, JENNIFER - Wellcome Trust Sanger Institute
item HAYWARD, ALEXANDER - Uppsala University
item HOWE, KERSTIN - Wellcome Trust Sanger Institute
item ZHI-LIANG, HU - Iowa State University
item HUMPHRAY, SEAN - Wellcome Trust Sanger Institute
item HUNT, TOBY - Wellcome Trust Sanger Institute
item HORNSHOJ, HENRIK - Aarhus University
item JEON, JIN-TAE - Gyeongsang National University
item JERN, PATRIC - Uppsala University
item JONES, MATTHEW - Wellcome Trust Sanger Institute
item JURKA, JERZY - Genetic Information Research Institute (GIRI)
item KANAMORI, HIROYUKI - Institute Of Japan Association For Technology In Agriculture, Forestry And Fisheries
item KAPETANOVIC, RONAN - University Of Edinburgh
item JAEBUM, KIM - Konkuk University
item KIM, JAE-HWAN - National Institute Of Animal Science
item KIM, KYU-WON - Seoul National University
item KIM, TAE-HUN - National Institute Of Animal Science
item LARSON, GREGER - University Of Durham
item LEE, KYOOYEOL - Konkuk University
item LEE, KYUNG-TAI - National Institute Of Animal Science
item LEGGETT, RICHARD - The Genome Analysis Centre
item LEWIN, HARRIS - University Of California
item LI, YINGRUI - Beijing Genome Institute
item LIU, WANSHENG - Pennsylvania State University
item LOVELAND, JANE - Wellcome Trust Sanger Institute
item LU, YAO - Beijing Genome Institute
item Lunney, Joan
item MA, JIAN - University Of Illinois
item MADSEN, OLE - Wageningen University
item Mann, Katherine
item MATHEWS, LUCY - Wellcome Trust Sanger Institute
item MCLAREN, STUART - Wellcome Trust Sanger Institute
item MOROZUMI, TAKEYA - Institute Of Japan Association For Technology In Agriculture, Forestry And Fisheries
item MURTAUG, MICHAEL - University Of Minnesota
item NARAYAN, JITENDRA - Aberystwyth University
item NGUYEN, DINH TRUONG - Konkuk University
item NI, PEIXIANG - Beijing Genome Institute
item OH, SONG-JUNG - Jeju National University
item ONTERU, SUNEEL - Iowa State University
item Rohrer, Gary

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/27/2012
Publication Date: 11/15/2012
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.