%0 Journal Article %J Nature %D 2022 %T Author Correction: Comparative and demographic analysis of orang-utan genomes. %A Locke, Devin P %A Hillier, LaDeana W %A Warren, Wesley C %A Kim C Worley %A Nazareth, Lynne V %A Donna M Muzny %A Yang, Shiaw-Pyng %A Wang, Zhengyuan %A Chinwalla, Asif T %A Minx, Pat %A Mitreva, Makedonka %A Cook, Lisa %A Delehaunty, Kim D %A Fronick, Catrina %A Schmidt, Heather %A Fulton, Lucinda A %A Fulton, Robert S %A Nelson, Joanne O %A Magrini, Vincent %A Pohl, Craig %A Graves, Tina A %A Markovic, Chris %A Cree, Andy %A Dinh, Huyen H %A Hume, Jennifer %A Kovar, Christie L %A Fowler, Gerald R %A Lunter, Gerton %A Meader, Stephen %A Heger, Andreas %A Ponting, Chris P %A Marques-Bonet, Tomas %A Alkan, Can %A Chen, Lin %A Cheng, Ze %A Kidd, Jeffrey M %A Eichler, Evan E %A White, Simon %A Searle, Stephen %A Vilella, Albert J %A Chen, Yuan %A Flicek, Paul %A Ma, Jian %A Raney, Brian %A Suh, Bernard %A Burhans, Richard %A Herrero, Javier %A Haussler, David %A Faria, Rui %A Fernando, Olga %A Darré, Fleur %A Farré, Domènec %A Gazave, Elodie %A Oliva, Meritxell %A Navarro, Arcadi %A Roberto, Roberta %A Capozzi, Oronzo %A Archidiacono, Nicoletta %A Della Valle, Giuliano %A Purgato, Stefania %A Rocchi, Mariano %A Konkel, Miriam K %A Walker, Jerilyn A %A Ullmer, Brygg %A Batzer, Mark A %A Smit, Arian F A %A Hubley, Robert %A Casola, Claudio %A Schrider, Daniel R %A Hahn, Matthew W %A Quesada, Victor %A Puente, Xose S %A Ordoñez, Gonzalo R %A López-Otín, Carlos %A Vinar, Tomas %A Brejova, Brona %A Ratan, Aakrosh %A Harris, Robert S %A Miller, Webb %A Kosiol, Carolin %A Lawson, Heather A %A Taliwal, Vikas %A Martins, André L %A Siepel, Adam %A Roychoudhury, Arindam %A Ma, Xin %A Degenhardt, Jeremiah %A Bustamante, Carlos D %A Gutenkunst, Ryan N %A Mailund, Thomas %A Dutheil, Julien Y %A Hobolth, Asger %A Schierup, Mikkel H %A Ryder, Oliver A %A Yoshinaga, Yuko %A De Jong, Pieter J %A Weinstock, George M %A Jeffrey Rogers %A Mardis, Elaine R %A Richard A Gibbs %A Wilson, Richard K %B Nature %V 608 %P E36 %8 2022 Aug %G eng %N 7924 %1 https://www.ncbi.nlm.nih.gov/pubmed/35962045?dopt=Abstract %R 10.1038/s41586-022-04799-7 %0 Journal Article %J Nature %D 2014 %T Gibbon genome and the fast karyotype evolution of small apes. %A Carbone, Lucia %A Harris, R Alan %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 Muzny, Donna M %A Warren, Wesley C %A Worley, Kim C %A Rogers, Jeffrey %A Wilson, Richard K %A Gibbs, Richard A %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 Nature %D 2011 %T Comparative and demographic analysis of orang-utan genomes. %A Locke, Devin P %A Hillier, LaDeana W %A Warren, Wesley C %A Worley, Kim C %A Nazareth, Lynne V %A Muzny, Donna M %A Yang, Shiaw-Pyng %A Wang, Zhengyuan %A Chinwalla, Asif T %A Minx, Pat %A Mitreva, Makedonka %A Cook, Lisa %A Delehaunty, Kim D %A Fronick, Catrina %A Schmidt, Heather %A Fulton, Lucinda A %A Fulton, Robert S %A Nelson, Joanne O %A Magrini, Vincent %A Pohl, Craig %A Graves, Tina A %A Markovic, Chris %A Cree, Andy %A Dinh, Huyen H %A Hume, Jennifer %A Kovar, Christie L %A Fowler, Gerald R %A Lunter, Gerton %A Meader, Stephen %A Heger, Andreas %A Ponting, Chris P %A Marques-Bonet, Tomas %A Alkan, Can %A Chen, Lin %A Cheng, Ze %A Kidd, Jeffrey M %A Eichler, Evan E %A White, Simon %A Searle, Stephen %A Vilella, Albert J %A Chen, Yuan %A Flicek, Paul %A Ma, Jian %A Raney, Brian %A Suh, Bernard %A Burhans, Richard %A Herrero, Javier %A Haussler, David %A Faria, Rui %A Fernando, Olga %A Darré, Fleur %A Farré, Domènec %A Gazave, Elodie %A Oliva, Meritxell %A Navarro, Arcadi %A Roberto, Roberta %A Capozzi, Oronzo %A Archidiacono, Nicoletta %A Della Valle, Giuliano %A Purgato, Stefania %A Rocchi, Mariano %A Konkel, Miriam K %A Walker, Jerilyn A %A Ullmer, Brygg %A Batzer, Mark A %A Smit, Arian F A %A Hubley, Robert %A Casola, Claudio %A Schrider, Daniel R %A Hahn, Matthew W %A Quesada, Victor %A Puente, Xose S %A Ordoñez, Gonzalo R %A López-Otín, Carlos %A Vinar, Tomas %A Brejova, Brona %A Ratan, Aakrosh %A Harris, Robert S %A Miller, Webb %A Kosiol, Carolin %A Lawson, Heather A %A Taliwal, Vikas %A Martins, André L %A Siepel, Adam %A Roychoudhury, Arindam %A Ma, Xin %A Degenhardt, Jeremiah %A Bustamante, Carlos D %A Gutenkunst, Ryan N %A Mailund, Thomas %A Dutheil, Julien Y %A Hobolth, Asger %A Schierup, Mikkel H %A Ryder, Oliver A %A Yoshinaga, Yuko %A De Jong, Pieter J %A Weinstock, George M %A Rogers, Jeffrey %A Mardis, Elaine R %A Gibbs, Richard A %A Wilson, Richard K %K Animals %K Centromere %K Cerebrosides %K Chromosomes %K Evolution, Molecular %K Female %K Gene Rearrangement %K Genetic Speciation %K Genetic Variation %K Genetics, Population %K Genome %K Humans %K Male %K Phylogeny %K Pongo abelii %K Pongo pygmaeus %K Population Density %K Population Dynamics %K Species Specificity %X

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

%B Nature %V 469 %P 529-33 %8 2011 Jan 27 %G eng %N 7331 %1 https://www.ncbi.nlm.nih.gov/pubmed/21270892?dopt=Abstract %R 10.1038/nature09687 %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