%0 Journal Article %J Science %D 2007 %T Evolutionary and biomedical insights from the rhesus macaque genome. %A Richard A Gibbs %A Jeffrey Rogers %A Katze, Michael G %A Bumgarner, Roger %A Weinstock, George M %A Mardis, Elaine R %A Remington, Karin A %A Strausberg, Robert L %A Venter, J Craig %A Wilson, Richard K %A Batzer, Mark A %A Bustamante, Carlos D %A Eichler, Evan E %A Hahn, Matthew W %A Hardison, Ross C %A Makova, Kateryna D %A Miller, Webb %A Milosavljevic, Aleksandar %A Palermo, Robert E %A Siepel, Adam %A Sikela, James M %A Attaway, Tony %A Bell, Stephanie %A Bernard, Kelly E %A Buhay, Christian J %A Chandrabose, Mimi N %A Dao, Marvin %A Davis, Clay %A Delehaunty, Kimberly D %A Ding, Yan %A Dinh, Huyen H %A Dugan-Rocha, Shannon %A Fulton, Lucinda A %A Gabisi, Ramatu Ayiesha %A Garner, Toni T %A Godfrey, Jennifer %A Hawes, Alicia C %A Hernandez, Judith %A Hines, Sandra %A Holder, Michael %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Ziad Khan %A Kirkness, Ewen F %A Cree, Andrew %A Fowler, R Gerald %A Lee, Sandra %A Lewis, Lora R %A Li, Zhangwan %A Liu, Yih-Shin %A Moore, Stephanie M %A Donna M Muzny %A Nazareth, Lynne V %A Ngo, Dinh Ngoc %A Okwuonu, Geoffrey O %A Pai, Grace %A Parker, David %A Paul, Heidie A %A Pfannkoch, Cynthia %A Pohl, Craig S %A Rogers, Yu-Hui %A Ruiz, San Juana %A Aniko Sabo %A Santibanez, Jireh %A Schneider, Brian W %A Smith, Scott M %A Sodergren, Erica %A Svatek, Amanda F %A Utterback, Teresa R %A Vattathil, Selina %A Warren, Wesley %A White, Courtney Sherell %A Chinwalla, Asif T %A Feng, Yucheng %A Halpern, Aaron L %A Hillier, LaDeana W %A Huang, Xiaoqiu %A Minx, Pat %A Nelson, Joanne O %A Pepin, Kymberlie H %A Xiang Qin %A Sutton, Granger G %A Venter, Eli %A Walenz, Brian P %A Wallis, John W %A Kim C Worley %A Yang, Shiaw-Pyng %A Jones, Steven M %A Marra, Marco A %A Rocchi, Mariano %A Schein, Jacqueline E %A Baertsch, Robert %A Clarke, Laura %A Csuros, Miklos %A Glasscock, Jarret %A R. Alan Harris %A Havlak, Paul %A Jackson, Andrew R %A Jiang, Huaiyang %A Liu, Yue %A Messina, David N %A Shen, Yufeng %A Song, Henry Xing-Zhi %A Wylie, Todd %A Zhang, Lan %A Birney, Ewan %A Han, Kyudong %A Konkel, Miriam K %A Lee, Jungnam %A Smit, Arian F A %A Ullmer, Brygg %A Wang, Hui %A Xing, Jinchuan %A Burhans, Richard %A Cheng, Ze %A Karro, John E %A Ma, Jian %A Raney, Brian %A She, Xinwei %A Cox, Michael J %A Demuth, Jeffery P %A Dumas, Laura J %A Han, Sang-Gook %A Hopkins, Janet %A Karimpour-Fard, Anis %A Kim, Young H %A Pollack, Jonathan R %A Vinar, Tomas %A Addo-Quaye, Charles %A Degenhardt, Jeremiah %A Denby, Alexandra %A Hubisz, Melissa J %A Indap, Amit %A Kosiol, Carolin %A Lahn, Bruce T %A Lawson, Heather A %A Marklein, Alison %A Nielsen, Rasmus %A Vallender, Eric J %A Clark, Andrew G %A Ferguson, Betsy %A Hernandez, Ryan D %A Hirani, Kashif %A Kehrer-Sawatzki, Hildegard %A Kolb, Jessica %A Patil, Shobha %A Pu, Ling-Ling %A Ren, Yanru %A Smith, David Glenn %A David A Wheeler %A Schenck, Ian %A Ball, Edward V %A Rui Chen %A Cooper, David N %A Giardine, Belinda %A Hsu, Fan %A Kent, W James %A Lesk, Arthur %A Nelson, David L %A O'brien, William E %A Prüfer, Kay %A Stenson, Peter D %A Wallace, James C %A Ke, Hui %A Liu, Xiao-Ming %A Wang, Peng %A Xiang, Andy Peng %A Yang, Fan %A Barber, Galt P %A Haussler, David %A Karolchik, Donna %A Kern, Andy D %A Kuhn, Robert M %A Smith, Kayla E %A Zwieg, Ann S %K Animals %K Biomedical Research %K Evolution, Molecular %K Female %K Gene Duplication %K Gene Rearrangement %K Genetic Diseases, Inborn %K Genetic Variation %K Genome %K Humans %K Macaca mulatta %K Male %K Multigene Family %K Mutation %K Pan troglodytes %K Sequence Analysis, DNA %K Species Specificity %X

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.

%B Science %V 316 %P 222-34 %8 2007 Apr 13 %G eng %N 5822 %1 https://www.ncbi.nlm.nih.gov/pubmed/17431167?dopt=Abstract %R 10.1126/science.1139247 %0 Journal Article %J Nature %D 2004 %T Genome sequence of the Brown Norway rat yields insights into mammalian evolution. %A Gibbs, Richard A %A Weinstock, George M %A Metzker, Michael L %A Muzny, Donna M %A Sodergren, Erica J %A Scherer, Steven %A Scott, Graham %A Steffen, David %A Worley, Kim C %A Burch, Paula E %A Okwuonu, Geoffrey %A Hines, Sandra %A Lewis, Lora %A DeRamo, Christine %A Delgado, Oliver %A Dugan-Rocha, Shannon %A Miner, George %A Morgan, Margaret %A Hawes, Alicia %A Gill, Rachel %A Holt, Robert A %A Adams, Mark D %A Amanatides, Peter G %A Baden-Tillson, Holly %A Barnstead, Mary %A Chin, Soo %A Evans, Cheryl A %A Ferriera, Steve %A Fosler, Carl %A Glodek, Anna %A Gu, Zhiping %A Jennings, Don %A Kraft, Cheryl L %A Nguyen, Trixie %A Pfannkoch, Cynthia M %A Sitter, Cynthia %A Sutton, Granger G %A Venter, J Craig %A Woodage, Trevor %A Smith, Douglas %A Lee, Hong-Mei %A Gustafson, Erik %A Cahill, Patrick %A Kana, Arnold %A Doucette-Stamm, Lynn %A Weinstock, Keith %A Fechtel, Kim %A Weiss, Robert B %A Dunn, Diane M %A Green, Eric D %A Blakesley, Robert W %A Bouffard, Gerard G %A De Jong, Pieter J %A Osoegawa, Kazutoyo %A Zhu, Baoli %A Marra, Marco %A Schein, Jacqueline %A Bosdet, Ian %A Fjell, Chris %A Jones, Steven %A Krzywinski, Martin %A Mathewson, Carrie %A Siddiqui, Asim %A Wye, Natasja %A McPherson, John %A Zhao, Shaying %A Fraser, Claire M %A Shetty, Jyoti %A Shatsman, Sofiya %A Geer, Keita %A Chen, Yixin %A Abramzon, Sofyia %A Nierman, William C %A Havlak, Paul H %A Chen, Rui %A Durbin, K James %A Simons, Rain %A Ren, Yanru %A Song, Xing-Zhi %A Li, Bingshan %A Liu, Yue %A Qin, Xiang %A Cawley, Simon %A Worley, Kim C %A Cooney, A J %A D'Souza, Lisa M %A Martin, Kirt %A Wu, Jia Qian %A Gonzalez-Garay, Manuel L %A Jackson, Andrew R %A Kalafus, Kenneth J %A McLeod, Michael P %A Milosavljevic, Aleksandar %A Virk, Davinder %A Volkov, Andrei %A Wheeler, David A %A Zhang, Zhengdong %A Bailey, Jeffrey A %A Eichler, Evan E %A Tuzun, Eray %A Birney, Ewan %A Mongin, Emmanuel %A Ureta-Vidal, Abel %A Woodwark, Cara %A Zdobnov, Evgeny %A Bork, Peer %A Suyama, Mikita %A Torrents, David %A Alexandersson, Marina %A Trask, Barbara J %A Young, Janet M %A Huang, Hui %A Wang, Huajun %A Xing, Heming %A Daniels, Sue %A Gietzen, Darryl %A Schmidt, Jeanette %A Stevens, Kristian %A Vitt, Ursula %A Wingrove, Jim %A Camara, Francisco %A Mar Albà, M %A Abril, Josep F %A Guigó, Roderic %A Smit, Arian %A Dubchak, Inna %A Rubin, Edward M %A Couronne, Olivier %A Poliakov, Alexander %A Hübner, Norbert %A Ganten, Detlev %A Goesele, Claudia %A Hummel, Oliver %A Kreitler, Thomas %A Lee, Young-Ae %A Monti, Jan %A Schulz, Herbert %A Zimdahl, Heike %A Himmelbauer, Heinz %A Lehrach, Hans %A Jacob, Howard J %A Bromberg, Susan %A Gullings-Handley, Jo %A Jensen-Seaman, Michael I %A Kwitek, Anne E %A Lazar, Jozef %A Pasko, Dean %A Tonellato, Peter J %A Twigger, Simon %A Ponting, Chris P %A Duarte, Jose M %A Rice, Stephen %A Goodstadt, Leo %A Beatson, Scott A %A Emes, Richard D %A Winter, Eitan E %A Webber, Caleb %A Brandt, Petra %A Nyakatura, Gerald %A Adetobi, Margaret %A Chiaromonte, Francesca %A Elnitski, Laura %A Eswara, Pallavi %A Hardison, Ross C %A Hou, Minmei %A Kolbe, Diana %A Makova, Kateryna %A Miller, Webb %A Nekrutenko, Anton %A Riemer, Cathy %A Schwartz, Scott %A Taylor, James %A Yang, Shan %A Zhang, Yi %A Lindpaintner, Klaus %A Andrews, T Dan %A Caccamo, Mario %A Clamp, Michele %A Clarke, Laura %A Curwen, Valerie %A Durbin, Richard %A Eyras, Eduardo %A Searle, Stephen M %A Cooper, Gregory M %A Batzoglou, Serafim %A Brudno, Michael %A Sidow, Arend %A Stone, Eric A %A Venter, J Craig %A Payseur, Bret A %A Bourque, Guillaume %A López-Otín, Carlos %A Puente, Xose S %A Chakrabarti, Kushal %A Chatterji, Sourav %A Dewey, Colin %A Pachter, Lior %A Bray, Nicolas %A Yap, Von Bing %A Caspi, Anat %A Tesler, Glenn %A Pevzner, Pavel A %A Haussler, David %A Roskin, Krishna M %A Baertsch, Robert %A Clawson, Hiram %A Furey, Terrence S %A Hinrichs, Angie S %A Karolchik, Donna %A Kent, William J %A Rosenbloom, Kate R %A Trumbower, Heather %A Weirauch, Matt %A Cooper, David N %A Stenson, Peter D %A Ma, Bin %A Brent, Michael %A Arumugam, Manimozhiyan %A Shteynberg, David %A Copley, Richard R %A Taylor, Martin S %A Riethman, Harold %A Mudunuri, Uma %A Peterson, Jane %A Guyer, Mark %A Felsenfeld, Adam %A Old, Susan %A Mockrin, Stephen %A Collins, Francis %K Animals %K Base Composition %K Centromere %K Chromosomes, Mammalian %K CpG Islands %K DNA Transposable Elements %K DNA, Mitochondrial %K Evolution, Molecular %K Gene Duplication %K Genome %K Genomics %K Humans %K Introns %K Male %K Mice %K Models, Molecular %K Mutagenesis %K Polymorphism, Single Nucleotide %K Rats %K Rats, Inbred BN %K Regulatory Sequences, Nucleic Acid %K Retroelements %K RNA Splice Sites %K RNA, Untranslated %K Sequence Analysis, DNA %K Telomere %X

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

%B Nature %V 428 %P 493-521 %8 2004 Apr 01 %G eng %N 6982 %1 https://www.ncbi.nlm.nih.gov/pubmed/15057822?dopt=Abstract %R 10.1038/nature02426