1 Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
2 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3 Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78227, USA.
4 Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
5 Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.
6 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
7 Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
8 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
9 Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
10 Department of Biology and School of Informatics, Indiana University, Bloomington, IN 47405, USA.
11 Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
12 Human Medical Genetics and Neuroscience Programs, Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
13 Department of Computer Science, Iowa State University, Ames, IA 50011, USA.
14 Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, BC, Canada.
15 Department of Genetics and Microbiology, University of Bari, Bari, Italy.
16 Department of Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95060, USA.
17 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
18 Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, QC H3C 3J7, Canada.
19 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103–8904, USA.
20 Center for Computation and Technology, Department of Computer Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
21 Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
22 Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
23 Department of Preventative Medicine and Biometrics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
24 Department of Pathology, Stanford University, Stanford, CA 94305, USA.
25 Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
26 Howard Hughes Medical Institute, Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
27 Institute of Biology, University of Copenhagen, Copenhagen DK-1017, Denmark.
28 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
29 Genetics Research and Informatics Program, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
30 Institute of Human Genetics, University of Ulm, Ulm, 89081, Germany.
31 Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
32 Department Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
33 Centre for Stem Cell Biology and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China.
34 South-China Primate Research and Development Center, Guangzhou 510080, China.
35 Howard Hughes Medical Institute, Santa Cruz, CA 95060, USA.
↵* To whom correspondence should be addressed. Richard A. Gibbs, E-mail: agibbs{at}bcm.edu
↵† All authors with their contributions and affiliations appear at the end of this paper.
7 Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
12 Human Medical Genetics and Neuroscience Programs, Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
7 Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
7 Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
7 Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
7 Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
7 Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
21 Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
12 Human Medical Genetics and Neuroscience Programs, Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
12 Human Medical Genetics and Neuroscience Programs, Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
12 Human Medical Genetics and Neuroscience Programs, Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
By Richard A. Gibbs, Jeffrey Rogers, Michael G. Katze, Roger Bumgarner, George M. Weinstock, Elaine R. Mardis, Karin A. Remington, Robert L. Strausberg, J. Craig Venter, Richard K. Wilson, Mark A. Batzer, Carlos D. Bustamante, Evan E. Eichler, Matthew W. Hahn, Ross C. Hardison, Kateryna D. Makova, Webb Miller, Aleksandar Milosavljevic, Robert E. Palermo, Adam Siepel, James M. Sikela, Tony Attaway, Stephanie Bell, Kelly E. Bernard, Christian J. Buhay, Mimi N. Chandrabose, Marvin Dao, Clay Davis, Kimberly D. Delehaunty, Yan Ding, Huyen H. Dinh, Shannon Dugan-Rocha, Lucinda A. Fulton, Ramatu Ayiesha Gabisi, Toni T. Garner, Jennifer Godfrey, Alicia C. Hawes, Judith Hernandez, Sandra Hines, Michael Holder, Jennifer Hume, Shalini N. Jhangiani, Vandita Joshi, Ziad Mohid Khan, Ewen F. Kirkness, Andrew Cree, R. Gerald Fowler, Sandra Lee, Lora R. Lewis, Zhangwan Li, Yih-shin Liu, Stephanie M. Moore, Donna Muzny, Lynne V. Nazareth, Dinh Ngoc Ngo, Geoffrey O. Okwuonu, Grace Pai, David Parker, Heidie A. Paul, Cynthia Pfannkoch, Craig S. Pohl, Yu-Hui Rogers, San Juana Ruiz, Aniko Sabo, Jireh Santibanez, Brian W. Schneider, Scott M. Smith, Erica Sodergren, Amanda F. Svatek, Teresa R. Utterback, Selina Vattathil, Wesley Warren, Courtney Sherell White, Asif T. Chinwalla, Yucheng Feng, Aaron L. Halpern, LaDeana W. Hillier, Xiaoqiu Huang, Pat Minx, Joanne O. Nelson, Kymberlie H. Pepin, Xiang Qin, Granger G. Sutton, Eli Venter, Brian P. Walenz, John W. Wallis, Kim C. Worley, Shiaw-Pyng Yang, Steven M. Jones, Marco A. Marra, Mariano Rocchi, Jacqueline E. Schein, Robert Baertsch, Laura Clarke, Miklós Csürös, Jarret Glasscock, R. Alan Harris, Paul Havlak, Andrew R. Jackson, Huaiyang Jiang, Yue Liu, David N. Messina, Yufeng Shen, Henry Xing-Zhi Song, Todd Wylie, Lan Zhang, Ewan Birney, Kyudong Han, Miriam K. Konkel, Jungnam Lee, Arian F. A. Smit, Brygg Ullmer, Hui Wang, Jinchuan Xing, Richard Burhans, Ze Cheng, John E. Karro, Jian Ma, Brian Raney, Xinwei She, Michael J. Cox, Jeffery P. Demuth, Laura J. Dumas, Sang-Gook Han, Janet Hopkins, Anis Karimpour-Fard, Young H. Kim, Jonathan R. Pollack, Tomas Vinar, Charles Addo-Quaye, Jeremiah Degenhardt, Alexandra Denby, Melissa J. Hubisz, Amit Indap, Carolin Kosiol, Bruce T. Lahn, Heather A. Lawson, Alison Marklein, Rasmus Nielsen, Eric J. Vallender, Andrew G. Clark, Betsy Ferguson, Ryan D. Hernandez, Kashif Hirani, Hildegard Kehrer-Sawatzki, Jessica Kolb, Shobha Patil, Ling-Ling Pu, Yanru Ren, David Glenn Smith, David A. Wheeler, Ian Schenck, Edward V. Ball, Rui Chen, David N. Cooper, Belinda Giardine, Fan Hsu, W. James Kent, Arthur Lesk, David L. Nelson, William E. O'Brien, Kay Prüfer, Peter D. Stenson, James C. Wallace, Hui Ke, Xiao-Ming Liu, Peng Wang, Andy Peng Xiang, Fan Yang, Galt P. Barber, David Haussler, Donna Karolchik, Andy D. Kern, Robert M. Kuhn, Kayla E. Smith, Ann S. Zwieg
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
By Richard A. Gibbs, Jeffrey Rogers, Michael G. Katze, Roger Bumgarner, George M. Weinstock, Elaine R. Mardis, Karin A. Remington, Robert L. Strausberg, J. Craig Venter, Richard K. Wilson, Mark A. Batzer, Carlos D. Bustamante, Evan E. Eichler, Matthew W. Hahn, Ross C. Hardison, Kateryna D. Makova, Webb Miller, Aleksandar Milosavljevic, Robert E. Palermo, Adam Siepel, James M. Sikela, Tony Attaway, Stephanie Bell, Kelly E. Bernard, Christian J. Buhay, Mimi N. Chandrabose, Marvin Dao, Clay Davis, Kimberly D. Delehaunty, Yan Ding, Huyen H. Dinh, Shannon Dugan-Rocha, Lucinda A. Fulton, Ramatu Ayiesha Gabisi, Toni T. Garner, Jennifer Godfrey, Alicia C. Hawes, Judith Hernandez, Sandra Hines, Michael Holder, Jennifer Hume, Shalini N. Jhangiani, Vandita Joshi, Ziad Mohid Khan, Ewen F. Kirkness, Andrew Cree, R. Gerald Fowler, Sandra Lee, Lora R. Lewis, Zhangwan Li, Yih-shin Liu, Stephanie M. Moore, Donna Muzny, Lynne V. Nazareth, Dinh Ngoc Ngo, Geoffrey O. Okwuonu, Grace Pai, David Parker, Heidie A. Paul, Cynthia Pfannkoch, Craig S. Pohl, Yu-Hui Rogers, San Juana Ruiz, Aniko Sabo, Jireh Santibanez, Brian W. Schneider, Scott M. Smith, Erica Sodergren, Amanda F. Svatek, Teresa R. Utterback, Selina Vattathil, Wesley Warren, Courtney Sherell White, Asif T. Chinwalla, Yucheng Feng, Aaron L. Halpern, LaDeana W. Hillier, Xiaoqiu Huang, Pat Minx, Joanne O. Nelson, Kymberlie H. Pepin, Xiang Qin, Granger G. Sutton, Eli Venter, Brian P. Walenz, John W. Wallis, Kim C. Worley, Shiaw-Pyng Yang, Steven M. Jones, Marco A. Marra, Mariano Rocchi, Jacqueline E. Schein, Robert Baertsch, Laura Clarke, Miklós Csürös, Jarret Glasscock, R. Alan Harris, Paul Havlak, Andrew R. Jackson, Huaiyang Jiang, Yue Liu, David N. Messina, Yufeng Shen, Henry Xing-Zhi Song, Todd Wylie, Lan Zhang, Ewan Birney, Kyudong Han, Miriam K. Konkel, Jungnam Lee, Arian F. A. Smit, Brygg Ullmer, Hui Wang, Jinchuan Xing, Richard Burhans, Ze Cheng, John E. Karro, Jian Ma, Brian Raney, Xinwei She, Michael J. Cox, Jeffery P. Demuth, Laura J. Dumas, Sang-Gook Han, Janet Hopkins, Anis Karimpour-Fard, Young H. Kim, Jonathan R. Pollack, Tomas Vinar, Charles Addo-Quaye, Jeremiah Degenhardt, Alexandra Denby, Melissa J. Hubisz, Amit Indap, Carolin Kosiol, Bruce T. Lahn, Heather A. Lawson, Alison Marklein, Rasmus Nielsen, Eric J. Vallender, Andrew G. Clark, Betsy Ferguson, Ryan D. Hernandez, Kashif Hirani, Hildegard Kehrer-Sawatzki, Jessica Kolb, Shobha Patil, Ling-Ling Pu, Yanru Ren, David Glenn Smith, David A. Wheeler, Ian Schenck, Edward V. Ball, Rui Chen, David N. Cooper, Belinda Giardine, Fan Hsu, W. James Kent, Arthur Lesk, David L. Nelson, William E. O'Brien, Kay Prüfer, Peter D. Stenson, James C. Wallace, Hui Ke, Xiao-Ming Liu, Peng Wang, Andy Peng Xiang, Fan Yang, Galt P. Barber, David Haussler, Donna Karolchik, Andy D. Kern, Robert M. Kuhn, Kayla E. Smith, Ann S. Zwieg
