Analyses of pig genomes provide insight into porcine demography and evolution

Nature

Volumn 491, Issue 7424, 2012, Pages 393-398

  Groenen, Martien A M ^a   Archibald, Alan L ^b   Uenishi, Hirohide ^c   Tuggle, Christopher K ^d   Takeuchi, Yasuhiro ^e   Rothschild, Max F ^d   Rogel Gaillard, Claire ^f   Park, Chankyu ^g   Milan, Denis ^h   Megens, Hendrik Jan ^a   Li, Shengting ^i,j   Larkin, Denis M ^k   Kim, Heebal ^l   Frantz, Laurent A F ^a   Caccamo, Mario ^m   Ahn, Hyeonju ^l   Aken, Bronwen L ⁿ   Anselmo, Anna ^o   Anthon, Christian ^p   Auvil, Loretta ^q   Badaoui, Bouabid ^o   Beattie, Craig W ^r   Bendixen, Christian ^j   Berman, Daniel ^s   Blecha, Frank ^t   Blomberg, Jonas ^u   Bolund, Lars ^i,j   Bosse, Mirte ^a   Botti, Sara ^o   Bujie, Zhan ^j   Bystrom, Megan ^d   Capitanu, Boris ^q   Carvalho Silva, Denise ^v   Chardon, Patrick ^f   Chen, Celine ^w   Cheng, Ryan ^d   Choi, Sang Haeng ^x   Chow, William ⁿ   Clark, Richard C ⁿ   Clee, Christopher ⁿ   Crooijmans, Richard P M A ^a   Dawson, Harry D ^w   Dehais, Patrice ^h   De Sapio, Fioravante ^b   Dibbits, Bert ^a   Drou, Nizar ^m   Du, Zhi Qiang ^d   Eversole, Kellye ^y   Fadista, Joao ^j,av   Fairley, Susan ⁿ   Faraut, Thomas ^h   Faulkner, Geoffrey J ^b,aw   Fowler, Katie E ^z   Fredholm, Merete ^p   Fritz, Eric ^d   Gilbert, James G R ⁿ   Giuffra, Elisabetta ^f,o   Gorodkin, Jan ^p   Griffin, Darren K ^z   Harrow, Jennifer L ⁿ   Hayward, Alexander ^aa   Howe, Kerstin ⁿ   Hu, Zhi Liang ^d   Humphray, Sean J ^n,ax   Hunt, Toby ⁿ   Hornshoøj, Henrik ^j   Jeon, Jin Tae ^ab   Jern, Patric ^aa   Jones, Matthew ⁿ   Jurka, Jerzy ^ac   Kanamori, Hiroyuki ^c,ad   Kapetanovic, Ronan ^b   Kim, Jaebum ^g,q   Kim, Jae Hwan ^ae   Kim, Kyu Won ^af   Kim, Tae Hun ^ae   Larson, Greger ^ag   Lee, Kyooyeol ^g   Lee, Kyung Tai ^ae   Leggett, Richard ^m   Lewin, Harris A ^ah   Li, Yingrui ⁱ   Liu, Wansheng ^ai   Loveland, Jane E ⁿ   Lu, Yao ⁱ   Lunney, Joan K ^s   Ma, Jian ^aj   Madsen, Ole ^a   Mann, Katherine ^s,ay   Matthews, Lucy ⁿ   McLaren, Stuart ⁿ   Morozumi, Takeya ^ad   Murtaugh, Michael P ^ak   Narayan, Jitendra ^k   Nguyen, Dinh Truong ^g   Ni, Peixiang ⁱ   Oh, Song Jung ^al   Onteru, Suneel ^d   Panitz, Frank ^j   Park, Eung Woo ^ae   Park, Hong Seog ^x   Pascal, Geraldine ^am   Paudel, Yogesh ^a   Perez Enciso, Miguel ^an   Ramirez Gonzalez, Ricardo ^m   Reecy, James M ^d   Rodriguez Zas, Sandra ^q   Rohrer, Gary A ^ao   Rund, Lauretta ^q   Sang, Yongming ^t   Schachtschneider, Kyle ^q   Schraiber, Joshua G ^ap   Schwartz, John ^ak   Scobie, Linda ^aq   Scott, Carol ⁿ   Searle, Stephen ⁿ   Servin, Bertrand ^h   Southey, Bruce R ^q   Sperber, Goran ^aa   Stadler, Peter ^ar   Sweedler, Jonathan V ^q   Tafer, Hakim ^ar   Thomsen, Bo ^j   Wali, Rashmi ^aq   Wang, Jian ⁱ   Wang, Jun ^i,as   White, Simon ⁿ   Xu, Xun ⁱ   Yerle, Martine ^h   Zhang, Guojie ^i,at   Zhang, Jianguo ⁱ   Zhang, Jie ^au   Zhao, Shuhong ^au   Rogers, Jane ^m   Churcher, Carol ⁿ   Schook, Lawrence B ^q   more..

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^d IOWA STATE UNIVERSITY   (United States)

^e MEDICAL RESEARCH COUNCIL   (United Kingdom)

^f AGROPARISTECH   (France)

^g Konkuk University   (South Korea)

^h CEMAGREF   (France)

ⁱ BGI SHENZHEN   (China)

^j AARHUS UNIVERSITY   (Denmark)

^k ABERYSTWYTH UNIVERSITY   (United Kingdom)

^l Seoul National University   (South Korea)

^m EARLHAM INSTITUTE   (United Kingdom)

ⁿ WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^o PARCO TECNOLOGICO PADANO   (Italy)

^p UNIVERSITY OF COPENHAGEN   (Denmark)

^q UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^r UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^s AGRICULTURAL RESEARCH SERVICE   (United States)

^t KANSAS STATE UNIVERSITY   (United States)

^u UPPSALA UNIVERSITY   (Sweden)

^v EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^w BELTSVILLE HUMAN NUTRITION RESEARCH CENTER   (United States)

^x Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^y Eversole Associates   (United States)

^z UNIVERSITY OF KENT   (United Kingdom)

^aa UPPSALA UNIVERSITY   (Sweden)

^ab Gyeongsang National University   (South Korea)

^ac Genetic Information Research Institute   (United States)

^ad Institute of Japan Association for Techno innovation in Agriculture   (Japan)

^ae National Institute of Animal Science   (South Korea)

^af CandK Genomics   (South Korea)

^ag DURHAM UNIVERSITY   (United Kingdom)

^ah UNIVERSITY OF CALIFORNIA   (United States)

^ai PENNSYLVANIA STATE UNIVERSITY   (United States)

^aj University of Illinois at Urbana Champaign   (United States)

^ak UNIVERSITY OF MINNESOTA   (United States)

^al Jeju National University   (South Korea)

^am UMR85 PHYSIOLOGIE DE LA REPRODUCTION ET DES COMPORTEMENTS   (France)

^an UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^ao AGRICULTURAL RESEARCH SERVICE   (United States)

^ap UNIVERSITY OF CALIFORNIA   (United States)

^aq GLASGOW CALEDONIAN UNIVERSITY   (United Kingdom)

^ar UNIVERSITY OF LEIPZIG   (Germany)

^as Capital Region   (Denmark)

^at University of Queensland ^*  (Denmark)

^au HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^av LUND UNIVERSITY DIABETES CENTRE   (Sweden)

^aw UNIVERSITY OF QUEENSLAND   (Australia)

^ax Illumina Inc   (United Kingdom)

^ay WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE STUDY; DEMOGRAPHIC SURVEY; EVOLUTIONARY BIOLOGY; GENOME; PHYLOGENETICS; PIG; RNA; SCAVENGING (FEEDING); WILD POPULATION;

ARTICLE; ASIA; COMPARATIVE STUDY; DOMESTIC PIG; EUROPE; GENETIC ASSOCIATION; GENETIC SELECTION; GENOME ANALYSIS; HUMAN; IMMUNE RESPONSE; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; OLFACTORY RECEPTOR; PHYLOGENY; PRIORITY JOURNAL; RNA PROCESSING; SMELLING; SOUTHEAST ASIA; WILD BOAR;

ANIMALS; DEMOGRAPHY; GENOME; MODELS, ANIMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POPULATION DYNAMICS; SUS SCROFA;

ASIA; EUROPE;

ANIMALIA; SUIDAE; SUS; SUS SCROFA; SUS SCROFA DOMESTICA;

EID: 84869003221     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature11622     Document Type: Article

References (45)

1. Kumar, S. & Hedges, S. B. A molecular timescale for vertebrate evolution. Nature 392, 917-920 (1998).
2. Meredith, R. W. et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334, 521-524 (2011).
3. Larson, G. et al.Worldwide phylogeography of wild boar revealsmultiple centers of pig domestication. Science 307, 1618-1621 (2005).
4. Schook, L. B. et al. Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome. Comp. Funct. Genomics 6, 251-255 (2005).
5. Archibald, A. L. et al. Pig genome sequence - analysis and publication strategy. BMC Genomics 11, 438 (2010).
6. Humphray, S. J. et al. A high utility integratedmapof the pig genome. GenomeBiol. 8, R139 (2007).
7. Flicek, P. et al. Ensembl 2012. Nucleic Acids Res. 40, D84-D90 (2012).
8. Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large genelists usingDAVIDbioinformatics resources.Nature Protocols 4, 44-57 (2009).
9. Barreiro, L. B. & Quintana-Murci, L. From evolutionary genetics to human immunology: how selection shapes host defense genes. Nature Rev. Genet. 11, 17-30 (2010).
10. Bovine Genome Sequencing and Analysis Consortium. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522-528 (2009).
11. Vandenbroeck, K. et al. Gene sequence, cDNA construction, expression in Escherichia coli and genetically approached purification of porcine interleukin-1 beta. Eur. J. Biochem. 217, 45-52 (1993).
12. Renard, C. et al. The genomic sequence and analysis of the swine major histocompatibility complex. Genomics 88, 96-110 (2006).
13. Tanaka-Matsuda, M., Ando, A., Rogel-Gaillard, C., Chardon, P. & Uenishi, H. Difference in number of loci of swine leukocyte antigen classical class I genes among haplotypes. Genomics 93, 261-273 (2009).
14. Schwartz, J. C., Lefranc, M. P. & Murtaugh, M. P. Evolution of the porcine (Sus scrofa domestica) immunoglobulin k locus through germline gene conversion. Immunogenetics 64, 303-311 (2012).
15. Schwartz, J. C., Lefranc, M. P. & Murtaugh, M. P. Organization, complexity and allelic diversity of the porcine (Sus scrofa domestica) immunoglobulin lambda locus. Immunogenetics 64, 399-407 (2012).
16. Uenishi, H. et al. Genomic structure aroundjoining segments and constant regions of swine T-cell receptor a/d (TRA/TRD) locus. Immunology 109, 515-526 (2003).
17. Uenishi, H. et al. Genomic sequence encoding diversity segments of the pig TCR d chain gene demonstrates productivity of highly diversified repertoire. Mol. Immunol. 46, 1212-1221 (2009).
18. Eguchi-Ogawa, T., Toki, D. & Uenishi, H. Genomic structure of the whole D-J-C clusters and the upstreamregion coding V segments of the TRB locus in pig. Dev. Comp. Immunol. 33, 1111-1119 (2009).
19. Sambrook, J. G. et al. Identification of a single killer immunoglobulin-like receptor (KIR) gene in the porcine leukocyte receptor complex on chromosome 6q. Immunogenetics 58, 481-486 (2006).
20. Nguyen, D. T. et al. The complete swine olfactory subgenome: expansion of olfactory receptor gene repertoire in the pig genome. BMC Genomics (in the press).
21. Shimamura, M., Abe, H., Nikaido, M., Ohshima, K. & Okada, N.Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs. Mol. Biol. Evol. 16, 1046-1060 (1999).
22. Hellekant, G. & Danilova, V. Taste in domestic pig, Sus scrofa. J. Anim. Physiol. Anim. Nutr. (Berl.) 82, 8-24 (1999).
23. Fischer, A., Gilad, Y., Man, O. & Pääbo, S. Evolution of bitter taste receptors in humans and apes. Mol. Biol. Evol. 22, 432-436 (2005).
24. Dong, D., Jones, G. & Zhang, S. Dynamic evolution of bitter taste receptor genes in vertebrates. BMC Evol. Biol. 9, 12 (2009).
25. Nelson, S. L. & Sanregret, J. D. Response of pigs to bitter-tasting compounds. Chem. Senses 22, 129-132 (1997).
26. Yokoyama, Y., Lambeck, K., De Deckker, P., Johnston, P. & Fifield, L. K. Timing of the Last Glacial Maximum. Nature 406, 713-716 (2000).
27. Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710-722 (2010).
28. Tortereau, F. et al. Sex specific differences in recombination rate in the pig are correlated with GC content. BMC Genomics (in the press).
29. Barton, N. H. Genetic hitchhiking. Phil. Trans. R. Soc. Lond. B 355, 1553-1562 (2000).
30. Lyttle, T. W. Cheaters sometimes prosper: distortion of mendelian segregation by meiotic drive. Trends Genet. 9, 205-210 (1993).
31. Ast, G. How did alternative splicing evolve? Nature Rev. Genet. 5, 773-782 (2004).
32. Garcia-Blanco, M. A., Baraniak, A. P. & Lasda, E. L. Alternative splicing in disease and therapy. Nature Biotechnol. 22, 535-546 (2004).
33. Kupsco, J. M., Wu, M.-J., Marzluff, W. F., Thapar, R. & Duronio, R. J. Genetic and biochemical characterization of Drosophila Snipper: A promiscuous member of the metazoan 39hExo/ERI-1 family of 39 to 59 exonucleases. RNA 12, 2103-2117 (2006).
34. Kennedy, S., Wang, D. & Ruvkun, G. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427, 645-649 (2004).
35. White, S. From globalized pig breeds to capitalist pigs: a study in animals cultures and evolutionary history. Environ. Hist. 16, 94-120 (2011).
36. Walters, E. M. et al. Completion of the swine genome will simplify the production of swine as a large animal biomedical model. BMC Med. Genomics (in the press).
37. Gillard, E. F. et al. A substitution of cysteine for arginine 614 in the ryanodine receptor is potentially causative of humanmalignant hyperthermia. Genomics 11, 751-755 (1991).
38. Murgiano, L., Tammen, I., Harlizius, B. & Drögemüller, C. A de novo germline mutation in MYH7 causes a progressive dominant myopathy in pigs. BMC Genomics (in the press).
39. Bosse, M. et al. Regions of homozygosity in the porcine genome: Consequence of demography and the recombination landscape. PLoS Genet. 8, e1003100(2012).
40. MacArthur, D. G. et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828 (2012).
41. Keinan, A. & Clark, A. G. Recent explosive humanpopulation growth has resulted in an excess of rare variants. Science 336, 740-743 (2012).
42. Paprotka, T. et al.Recombinant originof the retrovirusXMRV. Science333, 97-101 (2011).
43. Fang, X. et al. The sequence and analysis of an inbred pig genome. GigaScience (in the press).
44. Rubin, C. J. et al. Strong signatures of selection in the domestic pig genome. Proc. Natl. Acad. Sci. USA (in the press).
45. Li, H. & Durbin, R. Inference of human population history from individual wholegenome sequences. Nature 475, 493-496 (2011).