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4. Analyses of pig genomes provide insight into porcine demography and evolution

Author

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

Published
2012
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8. Gut microbiota Modulated by Probiotics and Garcinia cambogia Extract Correlate with Weight Gain and Adipocyte Sizes in High Fat-Fed Mice

Author

Heo, Jaeyoung, primary, Seo, Minseok, additional, Park, Hwanhee, additional, Lee, Woon Kyu, additional, Guan, Le Luo, additional, Yoon, Joon, additional, Caetano-Anolles, Kelsey, additional, Ahn, Hyeonju, additional, Kim, Se-Young, additional, Kang, Yoon-Mo, additional, Cho, Seoae, additional, and Kim, Heebal, additional

Published
2016
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11. Analyses of pig genomes provide insight into porcine demography and evolution

Author

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

Published
2012

12. Peeling Back the Evolutionary Layers of Molecular Mechanisms Responsive to Exercise-Stress in the Skeletal Muscle of the Racing Horse.

Author

Kim, Hyeongmin, Lee, Taeheon, Park, WonCheoul, Lee, Jin Woo, Kim, Jaemin, Lee, Bo-Young, Ahn, Hyeonju, Moon, Sunjin, Cho, Seoae, Do, Kyoung-Tag, Kim, Heui-Soo, Lee, Hak-Kyo, Lee, Chang-Kyu, Kong, Hong-Sik, Yang, Young-Mok, Park, Jongsun, Kim, Hak-Min, Kim, Byung Chul, Hwang, Seungwoo, and Bhak, Jong

Abstract

The modern horse (Equus caballus) is the product of over 50 million yrs of evolution. The athletic abilities of the horse have been enhanced during the past 6000 yrs under domestication. Therefore, the horse serves as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. The structure and function of skeletal muscle show remarkable plasticity to the physical and metabolic challenges following exercise. Here, we reveal an evolutionary layer of responsiveness to exercise-stress in the skeletal muscle of the racing horse. We analysed differentially expressed genes and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. By estimating genome-wide dN/dS ratios using six mammalian genomes, and FST and iHS using re-sequencing data derived from 20 horses, we were able to peel back the evolutionary layers of adaptations to exercise-stress in the horse. We found that the oldest and thickest layer (dN/dS) consists of system-wide tissue and organ adaptations. We further find that, during the period of horse domestication, the older layer (FST) is mainly responsible for adaptations to inflammation and energy metabolism, and the most recent layer (iHS) for neurological system process, cell adhesion, and proteolysis. [ABSTRACT FROM PUBLISHER]

Published
2013
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13. Analyses of pig genomes provide insight into porcine demography and evolution

Author

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

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.

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