%0 Journal Article %J Nature %D 2014 %T Gibbon genome and the fast karyotype evolution of small apes. %A Carbone, Lucia %A R. Alan Harris %A Gnerre, Sante %A Veeramah, Krishna R %A Lorente-Galdos, Belen %A Huddleston, John %A Meyer, Thomas J %A Herrero, Javier %A Roos, Christian %A Aken, Bronwen %A Anaclerio, Fabio %A Archidiacono, Nicoletta %A Baker, Carl %A Barrell, Daniel %A Batzer, Mark A %A Beal, Kathryn %A Blancher, Antoine %A Bohrson, Craig L %A Brameier, Markus %A Campbell, Michael S %A Capozzi, Oronzo %A Casola, Claudio %A Chiatante, Giorgia %A Cree, Andrew %A Damert, Annette %A De Jong, Pieter J %A Dumas, Laura %A Fernandez-Callejo, Marcos %A Flicek, Paul %A Fuchs, Nina V %A Gut, Ivo %A Gut, Marta %A Hahn, Matthew W %A Hernandez-Rodriguez, Jessica %A Hillier, LaDeana W %A Hubley, Robert %A Ianc, Bianca %A Izsvák, Zsuzsanna %A Jablonski, Nina G %A Johnstone, Laurel M %A Karimpour-Fard, Anis %A Konkel, Miriam K %A Kostka, Dennis %A Lazar, Nathan H %A Lee, Sandra L %A Lewis, Lora R %A Liu, Yue %A Locke, Devin P %A Mallick, Swapan %A Mendez, Fernando L %A Muffato, Matthieu %A Nazareth, Lynne V %A Nevonen, Kimberly A %A O'Bleness, Majesta %A Ochis, Cornelia %A Odom, Duncan T %A Pollard, Katherine S %A Quilez, Javier %A Reich, David %A Rocchi, Mariano %A Schumann, Gerald G %A Searle, Stephen %A Sikela, James M %A Skollar, Gabriella %A Smit, Arian %A Sonmez, Kemal %A ten Hallers, Boudewijn %A Terhune, Elizabeth %A Thomas, Gregg W C %A Ullmer, Brygg %A Ventura, Mario %A Walker, Jerilyn A %A Wall, Jeffrey D %A Walter, Lutz %A Ward, Michelle C %A Wheelan, Sarah J %A Whelan, Christopher W %A White, Simon %A Wilhelm, Larry J %A Woerner, August E %A Yandell, Mark %A Zhu, Baoli %A Hammer, Michael F %A Marques-Bonet, Tomas %A Eichler, Evan E %A Fulton, Lucinda %A Fronick, Catrina %A Donna M Muzny %A Warren, Wesley C %A Worley, Kim C %A Jeffrey Rogers %A Wilson, Richard K %A Richard A Gibbs %K Animals %K Evolution, Molecular %K Genome %K Hominidae %K Humans %K Hylobates %K Karyotype %K Molecular Sequence Data %K Phylogeny %K Retroelements %K Selection, Genetic %K Transcription Termination, Genetic %X

Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ∼5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.

%B Nature %V 513 %P 195-201 %8 2014 Sep 11 %G eng %N 7517 %1 https://www.ncbi.nlm.nih.gov/pubmed/25209798?dopt=Abstract %R 10.1038/nature13679 %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