Analyses of pig genomes provide insight into porcine demography and evolution

Katie Harvey; Darren K. Griffin; Kate Lee; Kate Lee; J. Ma; Elizabeth Park; M. Groenen; A. Archibald; H. Uenishi; C. Tuggle; Y. Takeuchi; M. Rothschild; C. Rogel-Gaillard; C. Park; D. Milan; H. Megens; S. Li; D. Larkin; H. Kim; L. Frantz; M. Caccamo; H. Ahn; B. Aken; A. Anselmo; C. Anthon; L. Auvil; B. Badaoui; C. Beattie; C. Bendixen; D. Berman; F. Blecha; J. Blomberg; L. Bolund; M. Bosse; S. Botti; Z. Bujie; M. Bystrom; B. Capitanu; D. Carvalho-Silva; P. Chardon; C. Chen; R. Cheng; S. Choi; W. Chow; R. Clark; C. Clee; R. Crooijmans; H. Dawson; P. Dehais; F. De Sapio; B. Dibbits; N. Drou; Z. Du; K. Eversole; J. Fadista; S. Fairley; T. Faraut; G. Faulkner; M. Fredholm; E. Fritz; J. Gilbert; E. Giuffra; J. Gorodkin; J. Harrow; A. Hayward; K. Howe; Z. Hu; S. Humphray; T. Hunt; H. Hornshøj; J. Jeon; P. Jern; M. Jones; J. Jurka; H. Kanamori; R. Kapetanovic; J. Kim; J. Kim; K. Kim; T. Kim; G. Larson; R. Leggett; H. Lewin; Y. Li; W. Liu; J. Loveland; Y. Lu; J. Lunney; O. Madsen; K. Mann; L. Matthews; S. McLaren; T. Morozumi; M. Murtaugh; J. Narayan; D. Truong Nguyen; P. Ni; S. Oh; S. Onteru; F. Panitz; H. Park; G. Pascal; Y. Paudel; M. Perez-Enciso; R. Ramirez-Gonzalez; J. Reecy; S. Rodriguez-Zas; G. Rohrer; L. Rund; Y. Sang; K. Schachtschneider; J. Schraiber; J. Schwartz; L. Scobie; C. Scott; S. Searle; B. Servin; B. Southey; G. Sperber; P. Stadler; J. Sweedler; H. Tafer; B. Thomsen; R. Wali; J. Wang; J. Wang; S. White; X. Xu; M. Yerle; G. Zhang; J. Zhang; J. Zhang; S. Zhao; J. Rogers; C. Churcher; L. Schook

doi:10.1038/nature11622

Analyses of pig genomes provide insight into porcine demography and evolution

Katie Harvey
, Darren K. Griffin
, Kate Lee
, Kate Lee
, J. Ma
, Elizabeth Park
, M. Groenen
, A. Archibald
, H. Uenishi
, C. Tuggle
, Y. Takeuchi
, M. Rothschild
, C. Rogel-Gaillard
, C. Park
, D. Milan
, H. Megens
, S. Li
, D. Larkin
, H. Kim
, L. Frantz

M. Caccamo, H. Ahn, B. Aken, A. Anselmo, C. Anthon, L. Auvil, B. Badaoui, C. Beattie, C. Bendixen, D. Berman, F. Blecha, J. Blomberg, L. Bolund, M. Bosse, S. Botti, Z. Bujie, M. Bystrom, B. Capitanu, D. Carvalho-Silva, P. Chardon, C. Chen, R. Cheng, S. Choi, W. Chow, R. Clark, C. Clee, R. Crooijmans, H. Dawson, P. Dehais, F. De Sapio, B. Dibbits, N. Drou, Z. Du, K. Eversole, J. Fadista, S. Fairley, T. Faraut, G. Faulkner, M. Fredholm, E. Fritz, J. Gilbert, E. Giuffra, J. Gorodkin, J. Harrow, A. Hayward, K. Howe, Z. Hu, S. Humphray, T. Hunt, H. Hornshøj, J. Jeon, P. Jern, M. Jones, J. Jurka, H. Kanamori, R. Kapetanovic, J. Kim, J. Kim, K. Kim, T. Kim, G. Larson, R. Leggett, H. Lewin, Y. Li, W. Liu, J. Loveland, Y. Lu, J. Lunney, O. Madsen, K. Mann, L. Matthews, S. McLaren, T. Morozumi, M. Murtaugh, J. Narayan, D. Truong Nguyen, P. Ni, S. Oh, S. Onteru, F. Panitz, H. Park, G. Pascal, Y. Paudel, M. Perez-Enciso, R. Ramirez-Gonzalez, J. Reecy, S. Rodriguez-Zas, G. Rohrer, L. Rund, Y. Sang, K. Schachtschneider, J. Schraiber, J. Schwartz, L. Scobie, C. Scott, S. Searle, B. Servin, B. Southey, G. Sperber, P. Stadler, J. Sweedler, H. Tafer, B. Thomsen, R. Wali, J. Wang, J. Wang, S. White, X. Xu, M. Yerle, G. Zhang, J. Zhang, J. Zhang, S. Zhao, J. Rogers, C. Churcher, L. Schook

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Pages (from-to)	393-398
Journal	Nature
Volume	491
Issue number	7424
DOIs	https://doi.org/10.1038/nature11622
Publication status	Published - 14 Nov 2012

Keywords

Genomics Genetics Evolution

Access to Document

10.1038/nature11622

Cite this

Harvey, K., Griffin, D. K., Lee, K., Lee, K., Ma, J., Park, E., Groenen, M., Archibald, A., Uenishi, H., Tuggle, C., Takeuchi, Y., Rothschild, M., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H., Li, S., Larkin, D., Kim, H., ... Schook, L. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491(7424), 393-398. https://doi.org/10.1038/nature11622

@article{333968bd4ee4446ba0d66910a4d6e816,

title = "Analyses of pig genomes provide insight into porcine demography and evolution",

abstract = "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.",

keywords = "Genomics Genetics Evolution",

author = "Katie Harvey and Griffin, \{Darren K.\} and Kate Lee and Kate Lee and J. Ma and Elizabeth Park and M. Groenen and A. Archibald and H. Uenishi and C. Tuggle and Y. Takeuchi and M. Rothschild and C. Rogel-Gaillard and C. Park and D. Milan and H. Megens and S. Li and D. Larkin and H. Kim and L. Frantz and M. Caccamo and H. Ahn and B. Aken and A. Anselmo and C. Anthon and L. Auvil and B. Badaoui and C. Beattie and C. Bendixen and D. Berman and F. Blecha and J. Blomberg and L. Bolund and M. Bosse and S. Botti and Z. Bujie and M. Bystrom and B. Capitanu and D. Carvalho-Silva and P. Chardon and C. Chen and R. Cheng and S. Choi and W. Chow and R. Clark and C. Clee and R. Crooijmans and H. Dawson and P. Dehais and \{De Sapio\}, F. and B. Dibbits and N. Drou and Z. Du and K. Eversole and J. Fadista and S. Fairley and T. Faraut and G. Faulkner and M. Fredholm and E. Fritz and J. Gilbert and E. Giuffra and J. Gorodkin and J. Harrow and A. Hayward and K. Howe and Z. Hu and S. Humphray and T. Hunt and H. Hornsh{\o}j and J. Jeon and P. Jern and M. Jones and J. Jurka and H. Kanamori and R. Kapetanovic and J. Kim and J. Kim and K. Kim and T. Kim and G. Larson and R. Leggett and H. Lewin and Y. Li and W. Liu and J. Loveland and Y. Lu and J. Lunney and O. Madsen and K. Mann and L. Matthews and S. McLaren and T. Morozumi and M. Murtaugh and J. Narayan and \{Truong Nguyen\}, D. and P. Ni and S. Oh and S. Onteru and F. Panitz and H. Park and G. Pascal and Y. Paudel and M. Perez-Enciso and R. Ramirez-Gonzalez and J. Reecy and S. Rodriguez-Zas and G. Rohrer and L. Rund and Y. Sang and K. Schachtschneider and J. Schraiber and J. Schwartz and L. Scobie and C. Scott and S. Searle and B. Servin and B. Southey and G. Sperber and P. Stadler and J. Sweedler and H. Tafer and B. Thomsen and R. Wali and J. Wang and J. Wang and S. White and X. Xu and M. Yerle and G. Zhang and J. Zhang and J. Zhang and S. Zhao and J. Rogers and C. Churcher and L. Schook",

year = "2012",

month = nov,

day = "14",

doi = "10.1038/nature11622",

language = "English",

volume = "491",

pages = "393--398",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7424",

}

Harvey, K, Griffin, DK, Lee, K , Lee, K, Ma, J, Park, E, Groenen, M, Archibald, A, Uenishi, H, Tuggle, C, Takeuchi, Y, Rothschild, M, Rogel-Gaillard, C, Park, C, Milan, D, Megens, H, Li, S, Larkin, D, Kim, H, Frantz, L, Caccamo, M, Ahn, H, Aken, B, Anselmo, A, Anthon, C, Auvil, L, Badaoui, B, Beattie, C, Bendixen, C, Berman, D, Blecha, F, Blomberg, J, Bolund, L, Bosse, M, Botti, S, Bujie, Z, Bystrom, M, Capitanu, B, Carvalho-Silva, D, Chardon, P, Chen, C, Cheng, R, Choi, S, Chow, W, Clark, R, Clee, C, Crooijmans, R, Dawson, H, Dehais, P, De Sapio, F, Dibbits, B, Drou, N, Du, Z, Eversole, K, Fadista, J, Fairley, S, Faraut, T, Faulkner, G, Fredholm, M, Fritz, E, Gilbert, J, Giuffra, E, Gorodkin, J, Harrow, J, Hayward, A, Howe, K, Hu, Z, Humphray, S, Hunt, T, Hornshøj, H, Jeon, J, Jern, P, Jones, M, Jurka, J, Kanamori, H, Kapetanovic, R, Kim, J, Kim, J, Kim, K, Kim, T, Larson, G, Leggett, R, Lewin, H, Li, Y, Liu, W, Loveland, J, Lu, Y, Lunney, J, Madsen, O, Mann, K, Matthews, L, McLaren, S, Morozumi, T, Murtaugh, M, Narayan, J, Truong Nguyen, D, Ni, P, Oh, S, Onteru, S, Panitz, F, Park, H, Pascal, G, Paudel, Y, Perez-Enciso, M, Ramirez-Gonzalez, R, Reecy, J, Rodriguez-Zas, S, Rohrer, G, Rund, L, Sang, Y, Schachtschneider, K, Schraiber, J, Schwartz, J, Scobie, L, Scott, C, Searle, S, Servin, B, Southey, B, Sperber, G, Stadler, P, Sweedler, J, Tafer, H, Thomsen, B, Wali, R, Wang, J, Wang, J, White, S, Xu, X, Yerle, M, Zhang, G, Zhang, J, Zhang, J, Zhao, S, Rogers, J, Churcher, C & Schook, L 2012, 'Analyses of pig genomes provide insight into porcine demography and evolution', Nature, vol. 491, no. 7424, pp. 393-398. https://doi.org/10.1038/nature11622

TY - JOUR

T1 - Analyses of pig genomes provide insight into porcine demography and evolution

AU - Harvey, Katie

AU - Griffin, Darren K.

AU - Lee, Kate

AU - Ma, J.

AU - Park, Elizabeth

AU - Groenen, M.

AU - Archibald, A.

AU - Uenishi, H.

AU - Tuggle, C.

AU - Takeuchi, Y.

AU - Rothschild, M.

AU - Rogel-Gaillard, C.

AU - Park, C.

AU - Milan, D.

AU - Megens, H.

AU - Li, S.

AU - Larkin, D.

AU - Kim, H.

AU - Frantz, L.

AU - Caccamo, M.

AU - Ahn, H.

AU - Aken, B.

AU - Anselmo, A.

AU - Anthon, C.

AU - Auvil, L.

AU - Badaoui, B.

AU - Beattie, C.

AU - Bendixen, C.

AU - Berman, D.

AU - Blecha, F.

AU - Blomberg, J.

AU - Bolund, L.

AU - Bosse, M.

AU - Botti, S.

AU - Bujie, Z.

AU - Bystrom, M.

AU - Capitanu, B.

AU - Carvalho-Silva, D.

AU - Chardon, P.

AU - Chen, C.

AU - Cheng, R.

AU - Choi, S.

AU - Chow, W.

AU - Clark, R.

AU - Clee, C.

AU - Crooijmans, R.

AU - Dawson, H.

AU - Dehais, P.

AU - De Sapio, F.

AU - Dibbits, B.

AU - Drou, N.

AU - Du, Z.

AU - Eversole, K.

AU - Fadista, J.

AU - Fairley, S.

AU - Faraut, T.

AU - Faulkner, G.

AU - Fredholm, M.

AU - Fritz, E.

AU - Gilbert, J.

AU - Giuffra, E.

AU - Gorodkin, J.

AU - Harrow, J.

AU - Hayward, A.

AU - Howe, K.

AU - Hu, Z.

AU - Humphray, S.

AU - Hunt, T.

AU - Hornshøj, H.

AU - Jeon, J.

AU - Jern, P.

AU - Jones, M.

AU - Jurka, J.

AU - Kanamori, H.

AU - Kapetanovic, R.

AU - Kim, J.

AU - Kim, K.

AU - Kim, T.

AU - Larson, G.

AU - Leggett, R.

AU - Lewin, H.

AU - Li, Y.

AU - Liu, W.

AU - Loveland, J.

AU - Lu, Y.

AU - Lunney, J.

AU - Madsen, O.

AU - Mann, K.

AU - Matthews, L.

AU - McLaren, S.

AU - Morozumi, T.

AU - Murtaugh, M.

AU - Narayan, J.

AU - Truong Nguyen, D.

AU - Ni, P.

AU - Oh, S.

AU - Onteru, S.

AU - Panitz, F.

AU - Park, H.

AU - Pascal, G.

AU - Paudel, Y.

AU - Perez-Enciso, M.

AU - Ramirez-Gonzalez, R.

AU - Reecy, J.

AU - Rodriguez-Zas, S.

AU - Rohrer, G.

AU - Rund, L.

AU - Sang, Y.

AU - Schachtschneider, K.

AU - Schraiber, J.

AU - Schwartz, J.

AU - Scobie, L.

AU - Scott, C.

AU - Searle, S.

AU - Servin, B.

AU - Southey, B.

AU - Sperber, G.

AU - Stadler, P.

AU - Sweedler, J.

AU - Tafer, H.

AU - Thomsen, B.

AU - Wali, R.

AU - Wang, J.

AU - White, S.

AU - Xu, X.

AU - Yerle, M.

AU - Zhang, G.

AU - Zhang, J.

AU - Zhao, S.

AU - Rogers, J.

AU - Churcher, C.

AU - Schook, L.

PY - 2012/11/14

Y1 - 2012/11/14

N2 - 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.

AB - 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.

KW - Genomics Genetics Evolution

U2 - 10.1038/nature11622

DO - 10.1038/nature11622

M3 - Article

SN - 0028-0836

VL - 491

SP - 393

EP - 398

JO - Nature

JF - Nature

IS - 7424

ER -

Analyses of pig genomes provide insight into porcine demography and evolution

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Keywords

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