Analyses of pig genomes provide insight into porcine demography and evolution

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  • Martien A M Groenen, Animal Breeding and Genomics Centre, Wageningen University, Holland
  • Alan L Archibald, The Roslin Institute and R(D)SVS, University of Edinburgh, Storbritannien
  • Hirohide Uenishi, National Institute of Agrobiological Sciences, Japan
  • Christopher K Tuggle, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Yasuhiro Takeuchi, MRC/UCL Centre for Medical Molecular Virology and Wohl Virion Centre, Division of Infection & Immunity, University College London, Storbritannien
  • Max F Rothschild, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Claire Rogel-Gaillard, INRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology/CEA, DSV, IRCM, Laboratoire de Radiobiologie et Etude du Ge´nome, Frankrig
  • Chankyu Park, Department of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul, Sydkorea
  • Denis Milan, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Storbritannien
  • Hendrik-Jan Megens, Animal Breeding and Genomics Centre, Wageningen University, Holland
  • Shengting Li, Danmark
  • Denis M Larkin, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Storbritannien
  • Heebal Kim, Department of Agricultural Biotechnology and C&K Genomics, Seoul National University, Sydkorea
  • Laurent A F Frantz, Animal Breeding and Genomics Centre, Wageningen University, Holland
  • Mario Caccamo, The Genome Analysis Centre, Norwich Research Park, Storbritannien
  • Hyeonju Ahn, Department of Agricultural Biotechnology and C&KGenomics, Seoul NationalUniversity, Sydkorea
  • Bronwen L Aken, Wellcome Trust Sanger Institute, WellcomeTrust Genome Campus, Storbritannien
  • Anna Anselmo, Parco Tecnologico Padano, Italien
  • Christian Anthon, Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Danmark
  • Loretta Auvil, Illinois Informatics Institute, University of Illinois, USA
  • Bouabid Badaoui, Parco Tecnologico Padano, Italien
  • Craig W Beattie, Department of Surgery, University of Illinois, USA
  • Christian Bendixen
  • Daniel Berman, USDA ARS BARC Animal Parasitic Diseases Laboratory, USA
  • Frank Blecha, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, USA
  • Jonas Blomberg, 22Clinical Virology, Department of Medical Sciences, Uppsala University, Sverige
  • Lars Bolund
  • Mirte Bosse, Animal Breeding and Genomics Centre, Wageningen University, Holland
  • Sara Botti, Parco Tecnologico Padano, Italien
  • Bujie Zhan
  • ,
  • Megan Bystrom, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Boris Capitanu, Illinois Informatics Institute, University of Illinois, USA
  • Denise Carvalho-Silva, European Bioinformatics Institute, Wellcome Trust Genome Campus, Storbritannien
  • Patrick Chardon, INRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology, Frankrig
  • Celine Chen, Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, United States Department of Agriculture, USA
  • Ryan Cheng, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Sang-Haeng Choi, Korean Research Institute of Bioscience and Biotechnology, Sydkorea
  • William Chow, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Richard C Clark, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Christopher Clee, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Richard P M A Crooijmans, Animal Breeding and Genomics Centre, Wageningen University, Holland
  • Harry D Dawson, Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, United States Department of Agriculture, BARC-East, USA
  • Patrice Dehais, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, Frankrig
  • Fioravante De Sapio, The Roslin Institute and R(D)SVS, University of Edinburgh, Storbritannien
  • Bert Dibbits, Animal Breeding and Genomics Centre, Wageningen University, Holland
  • Nizar Drou, The Genome Analysis Centre, Norwich Research Park, Storbritannien
  • Zhi-Qiang Du, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Kellye Eversole, Eversole Associates and the Alliance for Animal Genome Research, USA
  • João Fadista
  • ,
  • Susan Fairley, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Thomas Faraut, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, Frankrig
  • Geoffrey J Faulkner, The Roslin Institute and R(D)SVS, University of Edinburgh, Storbritannien
  • Katie E Fowler, The Roslin Institute and R(D)SVS, University of Edinburgh, Storbritannien
  • Merete Fredholm, Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Danmark
  • Eric Fritz, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • James G R Gilbert, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Elisabetta Giuffra, INRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology/CEA, DSV, IRCM, Laboratoire de Radiobiologie et Etude du Ge´nome, Frankrig
  • Jan Gorodkin, Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Danmark
  • Darren K Griffin, School of Biosciences, The University of Kent, Storbritannien
  • Jennifer L Harrow, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Alexander Hayward, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Sverige
  • Kerstin Howe, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Zhi-Liang Hu, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Sean J Humphray, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Toby Hunt, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Henrik Hornshøj, Danmark
  • Jin-Tae Jeon, Department of Animal Sciences, College of Agriculture and Life Sciences, Gyeongsang National University, Sydkorea
  • Patric Jern, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Sverige
  • Matthew Jones, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Jerzy Jurka, Genetic Information Research Institute, USA
  • Hiroyuki Kanamori, National Institute of Agrobiological Sciences, Japan
  • Ronan Kapetanovic, The Roslin Institute and R(D)SVS, University of Edinburgh, Storbritannien
  • Jaebum Kim, Department of Animal Biotechnology, Konkuk University, Sydkorea
  • Jae-Hwan Kim, Animal Genetic Resources Station, National Institute of Animal Science, Sydkorea
  • Kyu-Won Kim, C&K Genomics, Sydkorea
  • Tae-Hun Kim, 35Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Sydkorea
  • Greger Larson, Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Storbritannien
  • Kyooyeol Lee, Department of Animal Biotechnology, Konkuk University, Sydkorea
  • Kyung-Tai Lee, C&K Genomics, Sydkorea
  • Richard Leggett, The Genome Analysis Centre, Norwich Research Park, Storbritannien
  • Harris A Lewin, Department of Evolution and Ecology, The UC Davis Genome Center, USA
  • Yingrui Li, BGI-Shenzhen, Kina
  • Wansheng Liu, Department of Dairy and Animal Sciences, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, USA
  • Jane E Loveland, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Yao Lu, BGI-Shenzhen, Kina
  • Joan K Lunney, 0USDA ARS BARC Animal Parasitic Diseases Laboratory, USA
  • Jian Ma, Department of Bioengineering and Institute for Genomic Biology, University of Illinois, USA
  • Ole Madsen, Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, Holland
  • Katherine Mann, 0USDA ARS BARC Animal Parasitic Diseases Laboratory, USA
  • Lucy Matthews, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Stuart McLaren, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Takeya Morozumi, Institute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries, Japan
  • Michael P Murtaugh, Department of Veterinary and Biomedical Sciences, University of Minnesota, USA
  • Jitendra Narayan, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Storbritannien
  • Dinh Truong Nguyen, Department of Animal Biotechnology, Konkuk University, Sydkorea
  • Peixiang Ni, BGI-Shenzhen, Kina
  • Song-Jung Oh, Jeju National University, Sydkorea
  • Suneel Onteru, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Frank Panitz
  • Eung-Woo Park, Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Sydkorea
  • Hong-Seog Park, Korean Research Institute of Bioscience and Biotechnology, Sydkorea
  • Geraldine Pascal, INRA UMR85/CNRS UMR7247 Physiologie de la Reproduction et des Comportements/IFCE, Frankrig
  • Yogesh Paudel, Animal Breeding and Genomics Centre, Wageningen University, Holland
  • Miguel Perez-Enciso, ICREA, Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria UAB, Campus Universitat Autonoma Barcelona, Spanien
  • Ricardo Ramirez-Gonzalez, The Genome Analysis Centre, Norwich Research Park, Storbritannien
  • James M Reecy, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, USA
  • Sandra Rodriguez-Zas, Department of Animal Sciences, University of Illinois, USA
  • Gary A Rohrer, USDA, ARS, USMeat Animal Research Center, Clay Center, USA
  • Lauretta Rund, Department of Animal Sciences, University of Illinois, USA
  • Yongming Sang, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, USA
  • Kyle Schachtschneider, Department of Animal Sciences, University of Illinois, USA
  • Joshua G Schraiber, Department of Integrative Biology, University of California, USA
  • John Schwartz, Department of Veterinary and Biomedical Sciences, University of Minnesota, USA
  • Linda Scobie, Department of Life Sciences, Glasgow Caledonian University, Storbritannien
  • Carol Scott, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Stephen Searle, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Bertrand Servin, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, Frankrig
  • Bruce R Southey, Department of Animal Sciences, University of Illinois, USA
  • Goran Sperber, Department of Neuroscience, Biomedical Centre, Uppsala University, Sverige
  • Peter Stadler, Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Tyskland
  • Jonathan V Sweedler, Department of Chemistry, University of Illinois, USA
  • Hakim Tafer, Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Tyskland
  • Bo Thomsen
  • Rashmi Wali, Department of Life Sciences, Glasgow Caledonian University, Storbritannien
  • Jian Wang, BGI-Shenzhen, Kina
  • Jun Wang, BGI-Shenzhen, Kina
  • Simon White, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Xun Xu, BGI-Shenzhen, Kina
  • Martine Yerle, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, Frankrig
  • Guojie Zhang, BGI-Europe, Danmark
  • Jianguo Zhang, BGI-Shenzhen, Kina
  • Jie Zhang, Key Lab of Animal Genetics, Breeding, and Reproduction of Ministry Education, Huazhong Agricultural University, Kina
  • Shuhong Zhao, 53Key Lab of Animal Genetics, Breeding, and Reproduction of Ministry Education, Huazhong Agricultural University, Kina
  • Jane Rogers, The Genome Analysis Centre, Norwich Research Park, Storbritannien
  • Carol Churcher, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, Storbritannien
  • Lawrence B Schook, Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, USA
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.
OriginalsprogEngelsk
TidsskriftNature
Vol/bind491
Nummer7424
Sider (fra-til)393-398
Antal sider6
ISSN0028-0836
DOI
StatusUdgivet - 15 nov. 2012

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