%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 2006 %T The DNA sequence, annotation and analysis of human chromosome 3. %A Donna M Muzny %A Steven E Scherer %A Kaul, Rajinder %A Wang, Jing %A Yu, Jun %A Sudbrak, Ralf %A Buhay, Christian J %A Rui Chen %A Cree, Andrew %A Ding, Yan %A Dugan-Rocha, Shannon %A Gill, Rachel %A Gunaratne, Preethi %A R. Alan Harris %A Hawes, Alicia C %A Hernandez, Judith %A Hodgson, Anne V %A Hume, Jennifer %A Jackson, Andrew %A Ziad Khan %A Kovar-Smith, Christie %A Lewis, Lora R %A Lozado, Ryan J %A Metzker, Michael L %A Milosavljevic, Aleksandar %A Miner, George R %A Morgan, Margaret B %A Nazareth, Lynne V %A Scott, Graham %A Sodergren, Erica %A Song, Xing-Zhi %A Steffen, David %A Wei, Sharon %A David A Wheeler %A Wright, Mathew W %A Kim C Worley %A Yuan, Ye %A Zhang, Zhengdong %A Adams, Charles Q %A Ansari-Lari, M Ali %A Ayele, Mulu %A Brown, Mary J %A Chen, Guan %A Chen, Zhijian %A Clendenning, James %A Clerc-Blankenburg, Kerstin P %A Chen, Runsheng %A Chen, Zhu %A Davis, Clay %A Delgado, Oliver %A Dinh, Huyen H %A Dong, Wei %A Draper, Heather %A Ernst, Stephen %A Fu, Gang %A Gonzalez-Garay, Manuel L %A Garcia, Dawn K %A Gillett, Will %A Gu, Jun %A Hao, Bailin %A Haugen, Eric %A Havlak, Paul %A He, Xin %A Hennig, Steffen %A Hu, Songnian %A Huang, Wei %A Jackson, Laronda R %A Jacob, Leni S %A Kelly, Susan H %A Kube, Michael %A Levy, Ruth %A Li, Zhangwan %A Liu, Bin %A Liu, Jing %A Liu, Wen %A Lu, Jing %A Maheshwari, Manjula %A Nguyen, Bao-Viet %A Okwuonu, Geoffrey O %A Palmeiri, Anthony %A Pasternak, Shiran %A Perez, Lesette M %A Phelps, Karen A %A Plopper, Farah J H %A Qiang, Boqin %A Raymond, Christopher %A Rodriguez, Ruben %A Saenphimmachak, Channakhone %A Santibanez, Jireh %A Shen, Hua %A Shen, Yan %A Subramanian, Sandhya %A Tabor, Paul E %A Verduzco, Daniel %A Waldron, Lenée %A Wang, Jian %A Wang, Jun %A Wang, Qiaoyan %A Williams, Gabrielle A %A Wong, Gane K-S %A Yao, Zhijian %A Zhang, Jingkun %A Zhang, Xiuqing %A Zhao, Guoping %A Zhou, Jianling %A Zhou, Yang %A Nelson, David %A Lehrach, Hans %A Reinhardt, Richard %A Naylor, Susan L %A Yang, Huanming %A Olson, Maynard %A Weinstock, George %A Richard A Gibbs %K Animals %K Base Sequence %K Chromosome Breakage %K Chromosome Inversion %K Chromosomes, Human, Pair 3 %K Contig Mapping %K CpG Islands %K DNA, Complementary %K Evolution, Molecular %K Expressed Sequence Tags %K Human Genome Project %K Humans %K Macaca mulatta %K Molecular Sequence Data %K Pan troglodytes %K Sequence Analysis, DNA %K Synteny %X

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

%B Nature %V 440 %P 1194-8 %8 2006 Apr 27 %G eng %N 7088 %1 https://www.ncbi.nlm.nih.gov/pubmed/16641997?dopt=Abstract %R 10.1038/nature04728 %0 Journal Article %J Nature %D 2006 %T The finished DNA sequence of human chromosome 12. %A Scherer, Steven E %A Donna M Muzny %A Buhay, Christian J %A Rui Chen %A Cree, Andrew %A Ding, Yan %A Dugan-Rocha, Shannon %A Gill, Rachel %A Gunaratne, Preethi %A R. Alan Harris %A Hawes, Alicia C %A Hernandez, Judith %A Hodgson, Anne V %A Hume, Jennifer %A Jackson, Andrew %A Ziad Khan %A Kovar-Smith, Christie %A Lewis, Lora R %A Lozado, Ryan J %A Metzker, Michael L %A Milosavljevic, Aleksandar %A Miner, George R %A Montgomery, Kate T %A Morgan, Margaret B %A Nazareth, Lynne V %A Scott, Graham %A Sodergren, Erica %A Song, Xing-Zhi %A Steffen, David %A Lovering, Ruth C %A Wheeler, David A %A Worley, Kim C %A Yuan, Yi %A Zhang, Zhengdong %A Adams, Charles Q %A Ansari-Lari, M Ali %A Ayele, Mulu %A Brown, Mary J %A Chen, Guan %A Chen, Zhijian %A Clerc-Blankenburg, Kerstin P %A Davis, Clay %A Delgado, Oliver %A Dinh, Huyen H %A Draper, Heather %A Gonzalez-Garay, Manuel L %A Havlak, Paul %A Jackson, Laronda R %A Jacob, Leni S %A Kelly, Susan H %A Li, Li %A Li, Zhangwan %A Liu, Jing %A Liu, Wen %A Lu, Jing %A Maheshwari, Manjula %A Nguyen, Bao-Viet %A Okwuonu, Geoffrey O %A Pasternak, Shiran %A Perez, Lesette M %A Plopper, Farah J H %A Santibanez, Jireh %A Shen, Hua %A Tabor, Paul E %A Verduzco, Daniel %A Waldron, Lenée %A Wang, Qiaoyan %A Williams, Gabrielle A %A Zhang, Jingkun %A Zhou, Jianling %A Allen, Carlana C %A Amin, Anita G %A Anyalebechi, Vivian %A Bailey, Michael %A Barbaria, Joseph A %A Bimage, Kesha E %A Bryant, Nathaniel P %A Burch, Paula E %A Burkett, Carrie E %A Burrell, Kevin L %A Calderon, Eliana %A Cardenas, Veronica %A Carter, Kelvin %A Casias, Kristal %A Cavazos, Iracema %A Cavazos, Sandra R %A Ceasar, Heather %A Chacko, Joseph %A Chan, Sheryl N %A Chavez, Dean %A Christopoulos, Constantine %A Chu, Joseph %A Cockrell, Raynard %A Cox, Caroline D %A Dang, Michelle %A Dathorne, Stephanie R %A David, Robert %A Davis, Candi Mon'Et %A Davy-Carroll, Latarsha %A Deshazo, Denise R %A Donlin, Jeremy E %A D'Souza, Lisa %A Eaves, Kristy A %A Simons, Rain %A Emery-Cohen, Alexandra J %A Escotto, Michael %A Flagg, Nicole %A Forbes, Lisa D %A Gabisi, Abdul M %A Garza, Melissa %A Hamilton, Cerissa %A Henderson, Nicholas %A Hernandez, Omar %A Hines, Sandra %A Hogues, Marilyn E %A Huang, Mei %A Idlebird, DeVincent G %A Johnson, Rudy %A Jolivet, Angela %A Jones, Sally %A Kagan, Ryan %A King, Laquisha M %A Leal, Belita %A Lebow, Heather %A Lee, Sandra %A LeVan, Jaclyn M %A Lewis, Lakeshia C %A London, Pamela %A Lorensuhewa, Lorna M %A Loulseged, Hermela %A Lovett, Demetria A %A Lucier, Alice %A Lucier, Raymond L %A Ma, Jie %A Madu, Renita C %A Mapua, Patricia %A Martindale, Ashley D %A Martinez, Evangelina %A Massey, Elizabeth %A Mawhiney, Samantha %A Meador, Michael G %A Mendez, Sylvia %A Mercado, Christian %A Mercado, Iracema C %A Merritt, Christina E %A Miner, Zachary L %A Minja, Emmanuel %A Mitchell, Teresa %A Mohabbat, Farida %A Mohabbat, Khatera %A Montgomery, Baize %A Moore, Niki %A Morris, Sidney %A Munidasa, Mala %A Ngo, Robin N %A Nguyen, Ngoc B %A Nickerson, Elizabeth %A Nwaokelemeh, Ogechi O %A Nwokenkwo, Stanley %A Obregon, Melissa %A Oguh, Maryann %A Oragunye, Njideka %A Oviedo, Rodolfo J %A Parish, Bridgette J %A Parker, David N %A Parrish, Julia %A Parks, Kenya L %A Paul, Heidie A %A Payton, Brett A %A Perez, Agapito %A Perrin, William %A Pickens, Adam %A Primus, Eltrick L %A Pu, Ling-Ling %A Puazo, Maria %A Quiles, Miyo M %A Quiroz, Juana B %A Rabata, Dina %A Reeves, Kacy %A Ruiz, San Juana %A Shao, Hongmei %A Sisson, Ida %A Sonaike, Titilola %A Sorelle, Richard P %A Sutton, Angelica E %A Svatek, Amanda F %A Svetz, Leah Anne %A Tamerisa, Kavitha S %A Taylor, Tineace R %A Teague, Brian %A Thomas, Nicole %A Thorn, Rachel D %A Trejos, Zulma Y %A Trevino, Brenda K %A Ukegbu, Ogechi N %A Urban, Jeremy B %A Vasquez, Lydia I %A Vera, Virginia A %A Villasana, Donna M %A Wang, Ling %A Ward-Moore, Stephanie %A Warren, James T %A Wei, Xuehong %A White, Flower %A Williamson, Angela L %A Wleczyk, Regina %A Wooden, Hailey S %A Wooden, Steven H %A Yen, Jennifer %A Yoon, Lillienne %A Yoon, Vivienne %A Zorrilla, Sara E %A Nelson, David %A Kucherlapati, Raju %A Weinstock, George %A Richard A Gibbs %K Animals %K Base Composition %K Chromosomes, Human, Pair 12 %K CpG Islands %K Evolution, Molecular %K Expressed Sequence Tags %K Genes %K Humans %K Linkage Disequilibrium %K Microsatellite Repeats %K Molecular Sequence Data %K Mutagenesis, Insertional %K Pan troglodytes %K Sequence Analysis, DNA %K Sequence Deletion %K Short Interspersed Nucleotide Elements %K Synteny %X

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

%B Nature %V 440 %P 346-51 %8 2006 Mar 16 %G eng %N 7082 %1 https://www.ncbi.nlm.nih.gov/pubmed/16541075?dopt=Abstract %R 10.1038/nature04569