Study of cynomolgus monkey (Macaca fascicularis) Mhc DRB gene polymorphism in four populations

Immunogenetics

Volumn 64, Issue 8, 2012, Pages 605-614

  Blancher, Antoine ^a   Aarnink, Alice ^a   Tanaka, Keiko ^b   Ota, Masao ^c   Inoko, Hidetoshi ^b   Yamanaka, Hisashi ^d   Nakagawa, Hiroshi ^d   Apoil, Pol André ^a   Shiina, Takashi ^b  

^a UNIVERSITÉ PAUL SABATIER   (France)

^b TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^c SHINSHU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^d N   (Japan)

Author keywords

Cynomolgus macaque; DRB; MHC; Polymorphism

Indexed keywords

COMPLEMENTARY DNA; OLIGONUCLEOTIDE;

ARTICLE; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SEQUENCE; EXON; GENE; GENETIC POLYMORPHISM; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; INDONESIA; MACACA FASCICULARIS; MAJOR HISTOCOMPATIBILITY COMPLEX; MAURITIUS; MHC DRA GENE; MHC DRB GENE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHILIPPINES; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIET NAM;

ANIMALS; EXONS; GENES, MHC CLASS II; GENOTYPE; HAPLOTYPES; MACACA FASCICULARIS; PHILIPPINES; PHYLOGENY; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

ANIMALIA; MACACA FASCICULARIS;

EID: 84864286480     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-012-0613-5     Document Type: Article

References (26)

1. Aarnink A, Estrade L, Apoil PA, Kita YF, Saitou N, Shiina T, Blancher A (2010) Study of cynomolgus monkey (Macaca fascicularis) DRA polymorphism in four populations. Immunogenetics 62:123-136
2. Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, Babrzadeh F, Gharizadeh B, Luo M, Plummer FA, Kimani J, Carrington M, Middleton D, Rajalingam R, Beksac M, Marsh SG, Maiers M, Guethlein LA, Tavoularis S, Little AM, Green RE, Norman PJ, Parham P (2011) The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 334:89-94
3. Blancher A, Tisseyre P, Dutaur M, Apoil PA, Maurer C, Quesniaux V, Raulf F, Bigaud M, Abbal M (2006) Study of cynomolgus monkey (Macaca fascicularis) MhcDRB (Mafa-DRB) polymorphism in two populations. Immunogenetics 58:269-282 (Pubitemid 43673471)
4. Blancher A, Bonhomme M, Crouau-Roy B, Terao K, Kitano T, Saitou N (2008) Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis). J Hered 99:254-264
5. Bonhomme M, Blancher A, Cuartero S, Chikhi L, Crouau-Roy B (2008) Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data. Mol Ecol 17:1009-1019 (Pubitemid 351197369)
6. Bonhomme M, Cuartero S, Blancher A, Crouau-Roy B (2009) 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
7. Creager HM, Becker EA, Sandman KK, Karl JA, Lank SM, Bimber BN, Wiseman RW, Hughes AL, O'Connor SL, O'Connor DH (2011) Characterization of full-length MHC class II sequences in indonesian and vietnamese cynomolgus macaques. Immunogenetics 63:611-618
8. Diez-Rivero CM, Reche PA (2009) Discovery of conserved epitopes through sequence variability analysis. In: Flower DR, Davies M, Ranganathan S (eds) Bioinformatics for immunomics, vol 3. Springer, New York, pp 95-101
9. Doxiadis GG, de Groot N, Claas FH, Doxiadis II, van Rood JJ, Bontrop RE (2007) A highly divergent microsatellite facilitating fast and accurate DRB haplotyping in humans and rhesus macaques. Proc Natl Acad Sci USA 104:8907-8912 (Pubitemid 47175410)
10. Doxiadis GG, de Groot N, de Groot NG, Rotmans G, de Vos-Rouweler AJ, Bontrop RE (2010) Extensive DRB region diversity in cynomol-gus macaques: recombination as a driving force. Immunogenetics 62:137-147
11. Doxiadis GG, de Vos-Rouweler AJ, de Groot N, Otting N, Bontrop RE (2012) DR haplotype diversity of the cynomolgus macaque as defined by its transcriptome. Immunogenetics 64:31-37
12. Garcia-Boronat M, Diez-Rivero CM, Reinherz EL, Reche PA (2008) PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Res 36: W35-W41
13. Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, Jones PP, Parham P, Wakeland EK, Watkins DI (1990) Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 31:217-219 (Pubitemid 20132749)
14. Lekutis C, Letvin NL (1995) Biochemical and molecular characterization of rhesus monkey major histocompatibility complex class II DR. Hum Immunol 43:72-80
15. O'Connor SL, Blasky AJ, Pendley CJ, Becker EA, Wiseman RW, Karl JA, Hughes AL, O'Connor DH (2007) Comprehensive characterization of MHC class II haplotypes in mauritian cynomolgus macaques. Immunogenetics 59:449-462 (Pubitemid 46684717)
16. Reche P, Reinherz E (2003) Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J Mol Biol 331:623-641 (Pubitemid 36937150)
17. Robinson J, Waller MJ, Stoehr P, Marsh SG (2005) Ipd-the immuno polymorphism database. Nucleic Acids Res 33: D523-D526
18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
19. Shiina T, Tanaka K, Katsuyama Y, Otabe K, Sakamoto K, Kurata M, Nomura M, Yamanaka H, Nakagawa H, Inoko H, Ota M (2010) Mitochondrial DNA diversity among three subpopulations of cynomolgus macaques (Macaca fascicularis) originating from the Indochinese region. Exp Anim 59:567-578
20. Smith DG, McDonough JW, George DA (2007) 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 69:182-198 (Pubitemid 46232765)
21. Stevison LS, Kohn M (2009) Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques. Mol Ecol 18:2457-2475
22. Tamura K, Dudley J, Nei M, Kumar S (2007) Mega4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599 (Pubitemid 47236692)
23. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680 (Pubitemid 24354800)
24. Tosi AJ, Coke CS (2007) Comparative phylogenetics offer new insights into the biogeographic history of Macaca fascicularis and the origin of the Mauritian macaques. Mol Phylogenet Evol 42:498-504 (Pubitemid 44751522)
25. Tosi AJ, Morales JC, Melnick DJ (2002) Y-chromosome and mitochon-drial 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 (Pubitemid 34088651)
26. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Vogel HJ (ed) Evolving genes and proteins. Academic, New York