Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque

Genome Biology

Volumn 12, Issue 7, 2011, Pages

  Fang, Xiaodong ^a   Zhang, Yanfeng ^b,c   Zhang, Rui ^b,d   Yang, Lixin ^b,c   Li, Ming ^b,c   Ye, Kaixiong ^b   Guo, Xiaosen ^a   Wang, Jun ^a   Su, Bing ^b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d China National Center for Bioinformation   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARTICLE; CHINESE; CONTROLLED STUDY; GENE DELETION; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HETEROZYGOSITY; HOMOZYGOSITY; INDIAN; INTRON; MALE; NONHUMAN; PROMOTER REGION; RHESUS MONKEY; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; COMPUTER INTERFACE; DNA SEQUENCE; GENETICS; GENOME; INTERNET; MACACA MULATTA;

ANIMALIA; MACACA MULATTA; PRIMATES;

ANIMALS; DATABASES, GENETIC; GENOME; INTERNET; MACACA MULATTA; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; USER-COMPUTER INTERFACE;

EID: 79959912920     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-7-r63     Document Type: Article

References (37)

1. Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, Shoshani J, Gunnell G, Groves CP. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol Phylogenet Evol 1998, 9:585-598. 10.1006/mpev.1998.0495, 9668008.
2. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007, 316:222-234.
3. Colman RJ, Anderson RM, Johnson SC, Kastman EK, Kosmatka KJ, Beasley TM, Allison DB, Cruzen C, Simmons HA, Kemnitz JW, Weindruch R. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science 2009, 325:201-204. 10.1126/science.1173635, 2812811, 19590001.
4. Weiss RA. Polio vaccines exonerated. Nature 2001, 410:1035-1036. 10.1038/35074222, 11323649.
5. Yang SH, Cheng PH, Banta H, Piotrowska-Nitsche K, Yang JJ, Cheng EC, Snyder B, Larkin K, Liu J, Orkin J, Fang ZH, Smith Y, Bachevalier J, Zola SM, Li SH, Li XJ, Chan AW. Towards a transgenic model of Huntington's disease in a non-human primate. Nature 2008, 453:921-924. 10.1038/nature06975, 2652570, 18488016.
6. Chan AW, Yang SH. Generation of transgenic monkeys with human inherited genetic disease. Methods 2009, 49:78-84. 10.1016/j.ymeth.2009.05.007, 2752705, 19467335.
7. Disotell TR, Tosi AJ. The monkey's perspective. Genome Biol 2007, 8:226. 10.1186/gb-2007-8-9-226, 2375013, 17903312.
8. Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 2007, 316:240-243. 10.1126/science.1140462, 17431170.
9. Trichel AM, Rajakumar PA, Murphey-Corb M. Species-specific variation in SIV disease progression between Chinese and Indian subspecies of rhesus macaque. J Med Primatol 2002, 31:171-178. 10.1034/j.1600-0684.2002.02003.x, 12390539.
10. Ling B, Veazey RS, Luckay A, Penedo C, Xu K, Lifson JD, Marx PA. SIV(mac) pathogenesis in rhesus macaques of Chinese and Indian origin compared with primary HIV infections in humans. Aids 2002, 16:1489-1496. 10.1097/00002030-200207260-00005, 12131186.
11. Satkoski J, Malhi RS, Kanthaswamy S, Tito RY, Malladi VS, Smith DG. Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics 2008, 9:256. 10.1186/1471-2164-9-256, 2443142, 18510772.
12. Rogers J, Garcia R, Shelledy W, Kaplan J, Arya A, Johnson Z, Bergstrom M, Novakowski L, Nair P, Vinson A, Newman D, Heckman G, Cameron J. An initial genetic linkage map of the rhesus macaque (Macaca mulatta) genome using human microsatellite loci. Genomics 2006, 87:30-38. 10.1016/j.ygeno.2005.10.004, 16321502.
13. Malhi RS, Sickler B, Lin D, Satkoski J, Tito RY, George D, Kanthaswamy S, Smith DG. MamuSNP: a resource for rhesus macaque (Macaca mulatta) genomics. PLOs ONE 2007, 2:e438. 10.1371/journal.pone.0000438, 1859839, 17487284.
14. Raveendran M, Harris RA, Milosavljevic A, Johnson Z, Shelledy W, Cameron J, Rogers J. Designing new microsatellite markers for linkage and population genetic analyses in rhesus macaques and other nonhuman primates. Genomics 2006, 88:706-710. 10.1016/j.ygeno.2006.08.009, 17010566.
15. Ferguson B, Street SI, Wright H, Pearson C, Jia Y, Thompson SL, Allibone P, Dubay CJ, Spindel E, Norgren RB. Single nucleotide polymorphism (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta). BMC Genomics 2007, 8:43. 10.1186/1471-2164-8-43, 1803782, 17286860.
16. Khouangsathiene S, Pearson C, Street S, Ferguson B, Dubay C. MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms. Bioinformatics 2008, 24:2645-2646. 10.1093/bioinformatics/btn493, 2579713, 18796476.
17. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714. 10.1093/bioinformatics/btn025, 18227114.
18. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, et al. The diploid genome sequence of an Asian individual. Nature 2008, 456:60-65. 10.1038/nature07484, 2716080, 18987735.
19. Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF, Loftus B. Sequencing and analysis of an Irish human genome. Genome Biol 2010, 11:R91. 10.1186/gb-2010-11-9-r91, 2965383, 20822512.
20. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, et al. The diploid genome sequence of an Asian individual. Nature 2008, 456:60-65. 10.1038/nature07484, 2716080, 18987735.
21. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, et al. The diploid genome sequence of an individual human. PLoS Biol 2007, 5:e254. 10.1371/journal.pbio.0050254, 1964779, 17803354.
22. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
23. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 2009, 19:1527-1541. 10.1101/gr.091868.109, 2752135, 19546169.
24. Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Res 2009, 19:1553-1561. 10.1101/gr.092619.109, 2752137, 19602639.
25. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, et al. Ensembl 2009. Nucleic Acids Res 2009, 37:D690-697. 10.1093/nar/gkn828, 2686571, 19033362.
26. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008, 36:D901-906. 2238889, 18048412.
27. Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there?. Nat Rev Drug Discov 2006, 5:993-996. 10.1038/nrd2199, 17139284.
28. Jegga AG, Gowrisankar S, Chen J, Aronow BJ. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Res 2007, 35:D700-706. 10.1093/nar/gkl826, 1669724, 17142238.
29. CMSNP. , http://monkey.genomics.org.cn/
30. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res 2002, 12:1599-1610. 10.1101/gr.403602, 187535, 12368253.
31. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-158. 10.1093/nar/gkn221, 2238936, 17991681.
32. Loots G, Ovcharenko I. ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Bioinformatics 2007, 23:122-124. 10.1093/bioinformatics/btl546, 17090579.
33. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33:D514-517. 539987, 15608251.
34. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. The Pfam protein families database. Nucleic Acids Res 2008, 36:D281-288. 10.1093/nar/gkn226, 2238907, 18039703.
35. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
36. Gbrowse. , http://gmod.org/wiki/Gbrowse
37. Sequence Read Archive. , http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi