Single nucleotide polymorphisms (SNPs) are highly conserved in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Street, Summer L ^a,b   Kyes, Randall C ^b   Grant, Richard ^c   Ferguson, Betsy ^a,b  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c SNBL USA Ltd   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL CELL; ANIMAL GENETICS; ARTICLE; CHINA; DNA DETERMINATION; DNA MICROARRAY; DNA STRUCTURE; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE LOCATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC DIFFERENCE; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHICAL VARIATION (SPECIES); INDONESIA; MACACA; MAURITIUS; MITOCHONDRIAL GENETICS; MOLECULAR PHYLOGENY; NONHUMAN; PHILIPPINES; RHESUS MONKEY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; ASIA; COMPARATIVE STUDY; DEMOGRAPHY; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENCE;

MACACA; MACACA FASCICULARIS; MACACA MULATTA; PRIMATES;

ANIMALS; ASIA; BASE SEQUENCE; CONSERVED SEQUENCE; DEMOGRAPHY; MACACA FASCICULARIS; MACACA MULATTA; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 41149167691     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-480     Document Type: Article

References (37)

1. Cafaro A Caputo A Maggiorella MT Baroncelli S Fracasso C Pace M Borsetti A Sernicola L Negri DR Ten HP Betti M Michelini Z Macchia I Fanales-Belasio E Belli R Corrias F Butto S Verani P Titti F Ensoli B SHIV89.6P pathogenicity in cynomolgus monkeys and control of viral replication and disease onset by human immunodeficiency virus type 1 Tat vaccine J Med Primatol 2000, 29:193-208. 10.1034/ j.1600-0684.2000.290313.x 11085582
2. Reimann KA Parker RA Seaman MS Beaudry K Beddall M Peterson L Williams KC Veazey RS Montefiori DC Mascola JR Nabel GJ Letvin NL Pathogenicity of simian-human immunodeficiency virus SHIV-89.6P and SIVmac is attenuated in cynomolgus macaques and associated with early T-lymphocyte responses J Virol 2005, 79:8878-8885. 1168747 15994781 10.1128/ JVI.79.14.8878-8885.2005
3. Wiseman RW Wojcechowskyj JA Greene JM Blasky AJ Gopon T Soma T Friedrich TC O'Connor SL O'Connor DH Simian immunodeficiency virus SIVmac239 infection of major histocompatibility complex-identical cynomolgus macaques from Mauritius J Virol 2007, 81:349-361. 1797269 17035320 10.1128/JVI.01841-06
4. Rood PP Bottino R Balamurugan AN Smetanka C Ayares D Groth CG Murase N Cooper DK Trucco M Reduction of early graft loss after intraportal porcine islet transplantation in monkeys Transplantation 2007, 83:202-210. 10.1097/01.tp.0000250680.36942.c6 17264817
5. Kean LS Gangappa S Pearson TC Larsen CP Transplant tolerance in non-human primates: Progress, current challenges and unmet needs Am J Transplant 2006, 6:884-893. 10.1111/j.1600-6143.2006.01260.x 16611324
6. Gee MK Zhang L Rankin SE Collins JN Kauffman RF Wagner JD Rosiglitazone treatment improves insulin regulation and dyslipidemia in type 2 diabetic cynomolgus monkeys Metabolism 2004, 53:1121-1125. 10.1016/ j.metabol.2004.03.014 15334371
7. Grant KA Bennett AJ Advances in nonhuman primate alcohol abuse and alcoholism research Pharmacol Ther 2003, 100:235-255. 10.1016/ j.pharmthera.2003.08.004 14652112
8. 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 Dinh HH Dugan-Rocha S Fulton LA Gabisi RA Garner TT Godfrey J Hawes AC Hernandez J Hines S Holder M Hume J Jhangiani SN Joshi V Khan ZM Kirkness EF Cree A Fowler RG Lee S Lewis LR Li Z Liu YS Moore SM Muzny D Nazareth LV Ngo DN Okwuonu GO Pai G Parker D Paul HA Pfannkoch C Pohl CS Rogers YH Ruiz SJ Sabo A Santibanez J Schneider BW Smith SM Sodergren E Svatek AF Utterback TR Vattathil S Warren W White CS Chinwalla AT Feng Y Halpern AL Hillier LW Huang X Minx P Nelson JO Pepin KH Qin X Sutton GG Venter E Walenz BP Wallis JW Worley KC Yang SP Jones SM Marra MA Rocchi M Schein JE Baertsch R Clarke L Csuros M Glasscock J Harris RA Havlak P Jackson AR et al Evolutionary and biomedical insights from the rhesus macaque genome Science 2007, 316:222-234. 10.1126/science.1139247 17431167
9. 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
10. Ferguson B Street SL Wright H Pearson C Jia Y Thompson SL Allibone P Dubay CJ Spindel E Norgren RB Jr. Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta) BMC Genomics 2007, 8:43. 1803782 17286860 10.1186/1471-2164-8-43
11. 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
12. Kikuchi T Hara M Terao K Development of a microsatellite marker set applicable to genome-wide screening of cynomolgus monkeys (Macaca fascicularis) Primates 2007, 48:140-146. 10.1007/s10329-006-0008-z 17119865
13. Delson E Fossil macaques, phyletic relationships and a scenario of deployment The Macaques: Studies In Ecology, Behavior and Evolution New York, Van Nostrand Reinhold Lindburg DG 1980, 10-30.
14. Fooden J Classification and distribution of living macaques The Macaques: Studies in Ecology, Behavior and Evolution New York, Van Nostrand Reinhold Lindburg DG 1980, 1-9.
15. Fooden J Systematic review of the rhesus macaque, Macaca mulatta (Zimmerman, 1780). Field Museum of Natural History, Vol.96 Chicago, Fieldiana Publication 1509 2000, 180.
16. Abegg C Thierry B Macaque evolution and dispersal in insular south-east Asia. Biol J Linn Soc 2002. 75:555-576. 10.1046/j.1095-8312.2002.00045.x
17. Voris HK Maps of Pleistocene sea levels in southeast Asia: Shorelines, river systems and time durations J Biogeog 2000, 27:1153-1167. 10.1046/ j.1365-2699.2000.00489.x
18. Sussman RW Tattersall I Behavior and ecology of Macaca fascicularis in Mauritius: A preliminary study Primates 1981, 22:192-205. 10.1007/ BF02382610
19. Sussman RW Tattersall I Distribution, abundance and putative ecological strategy of Macaca fascularis on the island of Mauritius, southwestern Indian Ocean Folia Primatol 1986, 46:28-43.
20. Krebs KC Jin Z Rudersdorf R Hughes AL O'Connor DH Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques J Immunol 2005, 175:5230-5239. 16210628
21. O'Connor SL Blasky AJ Pendley CJ Becker EA Wiseman RW Karl JA Hughes AL O'Connor DH Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques Immunogenetics 2007, 59:449-462. 10.1007/ s00251-007-0209-7 17384942
22. Smith DG McDonough JW George DA Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques Am J Primatol 2007, 69:182-198. 10.1002/ajp.20337 17177314
23. Tosi AJ Coke CS Comparative phylogenetics offer new insights into the biogeographic history of Macaca fascicularis and the origin of the Mauritian macaques Mol Phylogenet Evol 2007, 42:498-504. 10.1016/ j.ympev.2006.08.002 16979912
24. Smith DG McDonough J Mitochondrial DNA variation in Chinese and Indian rhesus macaques (Macaca mulatta) Am J Primatol 2005, 65:1-25. 10.1002/ ajp.20094 15645455
25. Viray J Rolfs B Smith DG Comparison of the frequencies of major histocompatibility (MHC) class-II DQA1 and DQB1 alleles in Indian and Chinese rhesus macaques (Macaca mulatta) Comp Med 2001, 51:555-561. 11924820
26. Doxiadis GG Otting N de Groot NG Rouweler AJ Noort R Verschoor EJ Bontjer I Bontrop RE Evolutionary stability of MHC class II haplotypes in diverse rhesus macaque populations Immunogenetics 2003, 55:540-551. 10.1007/s00251-003-0590-9 14566434
27. Otting N de Vos-Rouweler AJ Heijmans CM de Groot NG Doxiadis GG Bontrop RE MHC class I A region diversity and polymorphism in macaque species Immunogenetics 2007, 59:367-375. 1914291 17334754 10.1007/ s00251-007-0201-2
28. Doxiadis GG Rouweler AJ de Groot NG Louwerse A Otting N Verschoor EJ Bontrop RE Extensive sharing of MHC class II alleles between rhesus and cynomolgus macaques Immunogenetics 2006, 58:259-268. 10.1007/ s00251-006-0083-8 16470376
29. Deinard A Smith DG Phylogenetic relationships among the macaques: evidence from the nuclear locus NRAMP1 J Hum Evol 2001, 41:45-59. 10.1006/jhev.2001.0480 11414773
30. Tosi AJ Morales JC Melnick DJ 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 2002, 23:161-178. 10.1023/A:1013258109954
31. Tosi AJ Morales JC Melnick DJ Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys Evolution Int J Org Evolution 2003, 57(6):1419-1435. 12894949
32. Hayasaka K Fujii K Horai S Molecular phylogeny of macaques: Implications of nucleotide sequences from an 896-base pair region of mitochondrial DNA Mol Biol Evol 1996, 13:1044-1053. 8752012
33. Morales JC Melnick DJ Phylogenetic relationships of the macaques (Cercopithecidae: Macaca), as revealed by high resolution restriction site mapping of mitochondrial ribosomal genes J Hum Evol 1998, 34:1-23. 10.1006/jhev.1997.0171 9467779
34. Baggiolini M Chemokines and leukocyte traffic Nature 1998, 392:565-568. 10.1038/33340 9560152
35. Craig IW The importance of stress and genetic variation in human aggression Bioessays 2007, 29:227-236. 10.1002/bies.20538 17295220
36. NCBI Single Nucleotide Polymorphism Database 2007 http://www.ncbi.nlm.nih.gov/SNP/
37. ONPRC Monkey SNP Database 2007 http://monkeysnp.ohsu.edu