Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

Nature Biotechnology

Volumn 29, Issue 11, 2011, Pages 1019-1023

  Yan, Guangmei ^a,b   Zhang, Guojie ^c   Fang, Xiaodong ^c   Zhang, Yanfeng ^d   Li, Cai ^c   Ling, Fei ^e   Cooper, David N ^f   Li, Qiye ^c,e   Li, Yan ^g   Van Gool, Alain J ^h   Du, Hongli ^e   Chen, Jiesi ^b   Chen, Ronghua ^h   Zhang, Pei ^c   Huang, Zhiyong ^c   Thompson, John R ^h   Meng, Yuhuan ^e   Bai, Yinqi ^c   Wang, Jufang ^e   Zhuo, Min ^e   Wang, Tao ^e   Huang, Ying ^c   Wei, Liqiong ^e   Li, Jianwen ^c   Wang, Zhiwen ^c   Hu, Haofu ^c   Yang, Pengcheng ^c   Le, Liang ^b   Stenson, Peter D ^f   Li, Bo ^c   Liu, Xiaoming ⁱ   Ball, Edward V ^f   An, Na ^c   Huang, Quanfei ^c   Zhang, Yong ^c   Fan, Wei ^c   Zhang, Xiuqing ^c   Li, Yingrui ^c   Wang, Wen ^d   Katze, Michael G ^j   Su, Bing ^d   Nielsen, Rasmus ^k   Yang, Huanming ^c   Wang, Jun ^c,k,l   Wang, Xiaoning ^a,e,m   Wang, Jian ^c   more..

^a South China Center for Innovative Pharmaceuticals   (China)

^b SUN YAT SEN UNIVERSITY   (China)

^c BGI SHENZHEN   (China)

^d KUNMING INSTITUTE OF ZOOLOGY   (China)

^e SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^f CARDIFF UNIVERSITY   (United Kingdom)

^g SICHUAN AGRICULTURAL UNIVERSITY   (China)

^h MERCK RESEARCH LABORATORIES   (United States)

ⁱ Guangdong Academy of Sciences   (China)

^j UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^k UNIVERSITY OF COPENHAGEN   (Denmark)

^l Capital Region   (Denmark)

^m CHINESE PLA GENERAL HOSPITAL   (China)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL MODEL; CHROMOSOMAL REARRANGEMENT; CLINICAL STUDY; DRUG TARGETS; GENETIC DIFFERENCES; GENETIC DIVERGENCE; GENETIC HETEROGENEITIES; GENOME SEQUENCES; GENOME SEQUENCING; HIGH QUALITY; HUMAN DISEASE; MEDICAL RESEARCH; NON-HUMAN PRIMATE; ORTHOLOGS; POSITIVE SELECTION; SEQUENCE SIMILARITY;

MAMMALS;

GENES;

ANIMAL GENETICS; ARTICLE; CHROMOSOME REARRANGEMENT; CONTROLLED STUDY; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENETIC DIFFERENCE; GENETIC HETEROGENEITY; MACACA; NONHUMAN; PRIMATE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BASE SEQUENCE; CHROMOSOME ABERRATIONS; EVOLUTION, MOLECULAR; GENOME; HUMANS; MACACA FASCICULARIS; MACACA MULATTA; MODELS, ANIMAL; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ANIMALIA; MACACA; MACACA MULATTA; PRIMATES;

EID: 80755189340     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.1992     Document Type: Article

References (27)

1. Carlsson, H.E., Schapiro, S.J., Farah, I. & Hau, J. Use of primates in research: a global overview. Am. J. Primatol. 63, 225-237 (2004). (Pubitemid 39211073)
2. Fooden, J. The Macaques: Studies in Ecology, Behavior, and Evolution (Van Nostrand-Reinhold, 1980).
3. Kumar, S. & Hedges, S.B. A molecular timescale for vertebrate evolution. Nature 392, 917-920 (1998). (Pubitemid 28232061)
4. Gibbs, R.A. et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234 (2007). (Pubitemid 46633091)
5. Bonhomme, M., Cuartero, S., Blancher, A. & Crouau-roy, B. Assessing natural introgression in 2 biomedical model species, the rhesus macaque (Macaca mulatta) and the long-tailed macaque (Macaca fascicularis). J. Hered. 100, 158-169 (2009).
6. Stevison, L.S. & Kohn, M.H. Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques. Mol. Ecol. 18, 2457-2475 (2009).
7. Tosi, A., Morales, J. & Melnick, D. Y-chromosome and mitochondrial markers in Macaca fascicularis indicate introgression with Indochinese M. mulatta and a biogeographic barrier in the Isthmus of Kra. Int. J. Primatol. 23, 161-178 (2002). (Pubitemid 34088651)
8. Hernandez, R.D. et al. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 316, 240-243 (2007). (Pubitemid 46633094)
9. Pool, J.E. & Nielsen, R. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181, 711-719 (2009).
10. Weinbauer, G. et al. Physiology and endocrinology of the ovarian cycle in macaques. Toxicol. Pathol. 36, 7S-23S (2008).
11. Palfree, R.G., Sadro, L.C. & Solomon, S. The gene encoding the human corticostatin HP-4 precursor contains a recent 86-base duplication and is located on chromosome 8. Mol. Endocrinol. 7, 199-205 (1993). (Pubitemid 23066862)
12. Wlasiuk, G. & Nachman, M.W. Adaptation and constraint at Toll-like receptors in primates. Mol. Biol. Evol. 27, 2172-2186 (2010).
13. Kosarac, B., Fox, A.A. & Collard, C.D. Effect of genetic factors on opioid action. Curr. Opin. Anaesthesiol. 22, 476-482 (2009).
14. Wolf, D. & Goff, S.P. Host restriction factors blocking retroviral replication. Annu. Rev. Genet. 42, 143-163 (2008).
15. Newman, R.M. et al. Evolution of a TRIM5-CypA splice isoform in old world monkeys. PLoS Pathogens 4, e1000003 (2008).
16. Yap, M.W., Nisole, S. & Stoye, J.P. A single amino acid change in the SPRY domain of human Trim5alpha leads to HIV-1 restriction. Curr. Biol. 15, 73-78 (2005). (Pubitemid 40084706)
17. Lim, S.Y. et al. TRIM5alpha modulates immunodeficiency virus control in rhesus monkeys. PLoS Pathog. 6, e1000738 (2010).
18. Brixen, K.T., Christensen, P.M., Ejersted, C. & Langdahl, B.L. Teriparatide (biosynthetic human parathyroid hormone 1-34): a new paradigm in the treatment of osteoporosis. Basic Clin. Pharmacol. Toxicol. 94, 260-270 (2004). (Pubitemid 38954892)
19. Chen, X., Ji, Z.L. & Chen, Y.Z. TTD: therapeutic target database. Nucleic Acids Res. 30, 412-415 (2002).
20. Cancilla, B., Davies, A., Cauchi, J.A., Risbridger, G.P. & Bertram, J.F. Fibroblast growth factor receptors and their ligands in the adult rat kidney. Kidney Int. 60, 147-155 (2001). (Pubitemid 32587549)
21. Khaitovich, P., Enard, W., Lachmann, M. & Paabo, S. Evolution of primate gene expression. Nat. Rev. Genet. 7, 693-702 (2006). (Pubitemid 44260005)
22. Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
23. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
24. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
25. Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124-1132 (2009).
26. Hudson, R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338 (2002). (Pubitemid 34183119)
27. Hudson, R.R., Kreitman, M. & Aguade, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153-159 (1987).