Analyses of pig genomes provide insight into porcine demography and evolution
Martien A. M. GroenenAnimal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands. [email protected]Alan ArchibaldThe Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.,Hirohide UenishiNational Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.,Christopher K. TuggleDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,Yasuhiro TakeuchiDivision of Infection & Immunity, MRC/UCL Centre for Medical Molecular Virology and Wohl Virion Centre, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK.,Max F. RothschildDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,Claire Rogel GaillardINRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology/CEA, DSV, IRCM, Laboratoire de Radiobiologie et Etude du Génome, Domaine de Vilvert, F-78350 Jouy-en-Josas, France.,Chankyu ParkDepartment of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, South Korea.,Denis MilanINRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.,Hendrik‐Jan MegensAnimal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Shengting LiBGI-Shenzhen, Shenzhen, 518083, ChinaDenis M. LarkinInstitute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK.,Heebal KimDepartment of Agricultural Biotechnology and C&K Genomics, Seoul National University, Gwanakgu, Seoul 151-742, South Korea.,Laurent FrantzAnimal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Mario CáccamoThe Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UKHyeonju AhnDepartment of Agricultural Biotechnology and C&K Genomics, Seoul National University, Gwanakgu, Seoul 151-742, South Korea.,Bronwen AkenWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Anna AnselmoParco Tecnologico Padano, Via Einstein, Loc. C. Codazza, 26900 Lodi, Italy.,Christian AnthonCenter for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, DenmarkLoretta AuvilIllinois Informatics Institute, University of Illinois, Urbana, 61801, Illinois, USABouabid BadaouiParco Tecnologico Padano, Via Einstein, Loc. C. Codazza, 26900 Lodi, Italy.,Craig W. BeattieDepartment of Surgery, University of Illinois, Chicago, 60612, Illinois, USAChristian BendixenDepartment of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, DenmarkDaniel BermanUSDA ARS BARC Animal Parasitic Diseases Laboratory, Beltsville, 20705, Maryland, USAFrank BlechaDepartment of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, 66506, Kansas, USAJonas BlombergDepartment of Medical Sciences, Clinical Virology, Uppsala University, Building D1, Academic Hospital, 751 85 Uppsala, Sweden.,Lars BolundBGI-Shenzhen, Shenzhen, 518083, ChinaMirte BosseAnimal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Sara BottiParco Tecnologico Padano, Via Einstein, Loc. C. Codazza, 26900 Lodi, Italy.,Bujie ZhanDepartment of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, DenmarkMegan BystromDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,Boris CapitanuIllinois Informatics Institute, University of Illinois, Urbana, 61801, Illinois, USADenise Carvalho‐SilvaEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UKPatrick ChardonINRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology/CEA, DSV, IRCM, Laboratoire de Radiobiologie et Etude du Génome, Domaine de Vilvert, F-78350 Jouy-en-Josas, France.,Celine ChenUnited States Department of Agriculture, Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, BARC-East 10300 Baltimore Ave Beltsville, Maryland 20705, USA.,Ryan P. ChengDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,Sang-Haeng ChoiKorean Research Institute of Bioscience and Biotechnology, 125 Gwahak ro, Yuseong gu, Daejeon 305-806, South Korea.,William ChowWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Richard ClarkWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Christopher CleeWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,R.P.M.A. CrooijmansAnimal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Harry DawsonUnited States Department of Agriculture, Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, BARC-East 10300 Baltimore Ave Beltsville, Maryland 20705, USA.,Patrice DéhaisINRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.,Fioravante De SapioThe Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.,Bert DibbitsAnimal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Nizar DrouThe Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UKZhiqiang DuDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,Kellye EversoleEversole Associates and the Alliance for Animal Genome Research, 5207 Wyoming Road, Bethesda, Maryland 20816, USA.,João FadistaDepartment of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, DenmarkSusan FairleyWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Thomas FarautINRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.,Geoffrey J. FaulknerThe Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.,Katie E. FowlerSchool of Biosciences, The University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UKMerete FredholmCenter for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, DenmarkEric FritzDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,James GilbertWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Elisabetta GiuffraINRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology/CEA, DSV, IRCM, Laboratoire de Radiobiologie et Etude du Génome, Domaine de Vilvert, F-78350 Jouy-en-Josas, France.,Jan GorodkinCenter for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, DenmarkDarren K. GriffinSchool of Biosciences, The University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UKJennifer HarrowWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Alexander HaywardDepartment of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, BMC, Box 582, SE75123 Uppsala, Sweden.,Kerstin HoweWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Zhi‐Liang HuDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,Sean HumphrayWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Toby HuntWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Henrik HornshøjDepartment of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, DenmarkJin‐Tae JeonDepartment of Animal Sciences, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, South Korea.,Patric JernDepartment of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, BMC, Box 582, SE75123 Uppsala, Sweden.,Matthew C. JonesWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Jerzy JurkaGenetic Information Research Institute, 1925 Landings Drive, Mountain View, 94043, California, USAHiroyuki KanamoriInstitute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan.,Ronan KapétanovicUniversity of EdinburghJaebum KimAnimal Genetic Resources Station, National Institute of Animal Science, RDA, San 4, Yongsanri, Unbong eup, Namwon 590-832, South Korea.,Jae-Hwan KimAnimal Genetic Resources Station, National Institute of Animal Science, RDA, San 4, Yongsanri, Unbong eup, Namwon 590-832, South Korea.,Kyuwon KimC&K Genomics, Gwanakgu, Seoul, 151-742, South KoreaTae-Hun KimAnimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 77 Chuksan gil, Kwonsun gu, Suwon 441-706, South Korea.,Greger LarsonDepartment of Archaeology, Durham Evolution and Ancient DNA, Durham University, Durham, DH1 3LE, UKKyooyeol LeeAnimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 77 Chuksan gil, Kwonsun gu, Suwon 441-706, South Korea.,Kyung‐Tai LeeAnimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 77 Chuksan gil, Kwonsun gu, Suwon 441-706, South Korea.,Richard M. LeggettThe Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UKHarris A. LewinDepartment of Evolution and Ecology, The UC Davis Genome Center, University of California, Davis, 95618, California, USAYingrui LiBGI-Shenzhen, Shenzhen, 518083, ChinaWansheng LiuDepartment of Dairy and Animal Sciences, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, 305 Henning Building, University Park, Pennsylvania 16802, USA.,Jane LovelandWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Yao LuBGI-Shenzhen, Shenzhen, 518083, ChinaJoan K. LunneyUSDA ARS BARC Animal Parasitic Diseases Laboratory, Beltsville, 20705, Maryland, USAJian MaDepartment of Bioengineering and Institute for Genomic Biology, University of Illinois, Urbana, 61801, Illinois, USAOle MadsenAnimal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.,Katherine MannUSDA ARS BARC Animal Parasitic Diseases Laboratory, Beltsville, 20705, Maryland, USALucy MatthewsWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Stuart McLarenWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Takeya MorozumiMichael P. MurtaughDepartment of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St Paul, Minnesota 55108, USA.,Jitendra NarayanInstitute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK.,Dinh Truong NguyenDepartment of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, South Korea.,Peixiang NiBGI-Shenzhen, Shenzhen, 518083, ChinaSong-Jung OhJeju National University, 102 Jejudaehakno, Jeju 690-756, South Korea.,Suneel Kumar OnteruDepartment of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames 50011, USA.,Frank PanitzDepartment of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, DenmarkEung-Woo ParkAnimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 77 Chuksan gil, Kwonsun gu, Suwon 441-706, South Korea.,
2012en
ABI
Аннотация
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. 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 extends the potential of the pig as a biomedical model. This study presents the assembly and analysis of the genome sequence of a female domestic Duroc pig and a comparison with the genomes of wild and domestic pigs from Europe and Asia; the results shed light on the evolutionary relationship between European and Asian wild boars. The domestic pig (Sus scrofa) is an important livestock species, its genome shaped by thousands of years of domestication and, latterly, sophisticated breeding practices. A high-quality draft genome sequence for a female domestic Duroc pig is published in this issue of Nature, under the auspices of the Swine Genome Sequencing Consortium. Comparisons of the genomes of wild and domestic pigs shed light on the evolutionary relationship between European and Asian wild boars, and reveal the rapid evolution of genes involved in the immune response and in olfaction. The authors identify many possible disease-causing gene variants, increasing the potential of the pig as a biomedical model, and present a detailed analysis of endogenous porcine retroviruses, knowledge of which is important for the possible use of pigs in xenotransplantation.
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