Retained orthologous relationships of the MHC class i genes during euteleost evolution

Molecular Biology and Evolution

Volumn 28, Issue 11, 2011, Pages 3099-3112

  Nonaka, Mayumi I ^a   Aizawa, Kouichi ^a   Mitani, Hiroshi ^a   Bannai, Hidemi P ^a   Nonaka, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

evolution; MHC class I gene; teleost

Indexed keywords

COMPLEMENTARY DNA; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1;

AMINO ACID SEQUENCE; ARTICLE; FISH; GENE; GENETIC LINKAGE; GENOME; HOST RESISTANCE; IMMUNE SYSTEM; IMMUNOGENETICS; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORYZIAS; PHYLOGENETIC TREE; PHYLOGENY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TELEOST;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA PRIMERS; EVOLUTION, MOLECULAR; GENES, MHC CLASS I; GENETIC LINKAGE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; ORYZIAS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ORYZIAS LATIPES; ORYZIINAE; PRIMATES; SALMONIDAE; TELEOSTEI; VERTEBRATA;

EID: 80155187381     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr139     Document Type: Article

References (54)

1. Adams EJ, Parham P. 2001. Species-specific evolution of MHC class I genes in the higher primates. Immunol Rev. 183:41-64.
2. Antao AB, Wilson M, Wang J, Bengten E, Miller NW, Clem LW, Chinchar VG. 2001. Genomic organization and differential expression of channel catfish MHC class I genes. Dev Comp Immunol. 25:579-595.
3. Aoyagi K, Dijkstra JM, Xia C, Denda I, Ototake M, Hashimoto K, Nakanishi T. 2002. Classical MHC class I genes composed of highly divergent sequence lineages share a single locus in rainbow trout (Oncorhynchus mykiss). J Immunol. 168:260-273.
4. Belov K, Deakin JE, Papenfuss AT, et al. (18 co-authors). 2006. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol. 4:e46.
5. Bingulac-Popovic J, Figueroa F, Sato A, Talbot WS, Johnson SL, Gates M, Postlethwait JH, Klein J. 1997. Mapping of mhc class I and class II regions to different linkage groups in the zebrafish, Danio rerio. Immunogenetics 46:129-134.
6. Clark MS, Shaw L, Kelly A, Snell P, Elgar G. 2001. Characterization of the MHC class I region of the Japanese pufferfish (Fugu rubripes). Immunogenetics 52:174-185.
7. Figueroa F, Mayer WE, Sato A, Zaleska-Rutczynska Z, Hess B, Tichy H, Klein J. 2001. Mhc class I genes of swordtail fishes, Xiphophorus: Variation in the number of loci and existence of ancient gene families. Immunogenetics 53:695-708.
8. Flajnik MF, Kasahara M. 2001. Comparative genomics of the MHC: Glimpses into the evolution of the adaptive immune system. Immunity 15:351-362.
9. Fujiki K, Booman M, Chin-Dixon E, Dixon B. 2001. Cloning and characterization of cDNA clones encoding membrane-bound and potentially secreted major histocompatibility class I receptors from walleye (Stizostedion vitreum). Immunogenetics 53:760-769.
10. Green EL. 1981. Linkage, recombination and mapping. In: Green E, editor. Genomics and probability in animal breeding experiments. New York: Macmillan. p. 77-113.
11. Grimholt U, Drablos F, Jorgensen SM, Hoyheim B, Stet RJ. 2002. The major histocompatibility class I locus in Atlantic salmon (Salmo salar L.): Polymorphism, linkage analysis and protein modelling. Immunogenetics 54:570-581.
12. Gunther E, Walter L. 2001. The major histocompatibility complex of the rat (Rattus norvegicus). Immunogenetics 53:520-542.
13. Katagiri T, Hirono I, Aoki T, Sakai M. 1996. Isolation of major histocompatibility complex class I cDNA from pink salmon (Oncorhynchus gorbuscha). Dev Comp Immunol. 20:217-228.
14. Kiryu I, Dijkstra JM, Sarder RI, Fujiwara A, Yoshiura Y, Ototake M. 2005. New MHC class Ia domain lineages in rainbow trout (Oncorhynchus mykiss) which are shared with other fish species. Fish Shellfish Immunol. 18:243-254.
15. Klein J, Sato A, Nikolaidis N. 2007. MHC, TSP, and the origin of species: From immunogenetics to evolutionary genetics. Annu Rev Genet. 41:281-304.
16. Kulski JK, Shiina T, Anzai T, Kohara S, Inoko H. 2002. Comparative genomic analysis of the MHC: The evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol Rev. 190:95-122.
17. Kumanovics A, Takada T, Lindahl KF. 2003. Genomic organization of the mammalian MHC. Annu Rev Immunol. 21:629-657.
18. Lukacs MF, Harstad H, Bakke HG, Beetz-Sargent M, McKinnel L, Lubieniecki KP, Koop BF, Grimholt U. 2010. Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon. BMC Genomics. 11:154.
19. Lukacs MF, Harstad H, Grimholt U, et al. (11 co-authors). 2007. Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar). BMC Genomics. 8:251.
20. Madden DR, Gorga JC, Strominger JL, Wiley DC. 1992. The threedimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC. Cell. 70:1035-1048.
21. Matsuo MY, Asakawa S, Shimizu N, Kimura H, Nonaka M. 2002. Nucleotide sequence of theMHC class I genomic region of a teleost, the medaka (Oryzias latipes). Immunogenetics 53:930-940.
22. Mehta RB, Nonaka MI, Nonaka M. 2009. Comparative genomic analysis of the major histocompatibility complex class I region in the teleost genus Oryzias. Immunogenetics 61:385-399.
23. Michalova V, Murray BW, Sultmann H, Klein J. 2000. A contig map of the Mhc class I genomic region in the zebrafish reveals ancient synteny. J Immunol. 164:5296-5305.
24. Miller KM, Kaukinen KH, Schulze AD. 2002. Expansion and contraction of major histocompatibility complex genes: A teleostean example. Immunogenetics 53:941-963.
25. Miller KM, Li S, Ming TJ, Kaukinen KH, Schulze AD. 2006. The salmonid MHC class I: More ancient loci uncovered. Immunogenetics 58:571-589.
26. Naruse K, Tanaka M, Mita K, Shima A, Postlethwait J, Mitani H. 2004. A medaka gene map: The trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res. 14:820-828.
27. Nei M, Gu X, Sitnikova T. 1997. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci U S A. 94:7799-7806.
28. Nonaka MI, Nonaka M. 2010. Evolutionary analysis of two classical MHC class I loci of the medaka fish, Oryzias latipes: Haplotypespecific genomic diversity, locus-specific polymorphisms, and interlocus homogenization. Immunogenetics 62:319-332.
29. Okamura K, Ototake M, Nakanishi T, Kurosawa Y, Hashimoto K. 1997. The most primitive vertebrates with jaws possess highly polymorphic MHC class I genes comparable to those of humans. Immunity 7:777-790.
30. Piontkivska H, Nei M. 2003. Birth-and-death evolution in primateMHC class I genes: Divergence time estimates. Mol Biol Evol. 20:601-609.
31. Rada C, Lorenzi R, Powis SJ, van den Bogaerde J, Parham P, Howard JC. 1990. Concerted evolution of class I genes in the major histocompatibility complex of murine rodents. Proc Natl Acad Sci U S A. 87:2167-2171.
32. Rodgers JR, Cook RG. 2005. MHC class Ib molecules bridge innate and acquired immunity. Nat Rev Immunol. 5:459-471.
33. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
34. Salter RD, Benjamin RJ, Wesley PK, Buxton SE, Garrett TP, Clayberger C, Krensky AM, Norment AM, Littman DR, Parham P. 1990. A binding site for the T-cell co-receptor CD8 on the alpha 3 domain of HLA-A2. Nature 345:41-46.
35. Sambrook JG, Figueroa F, Beck S. 2005. A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish. BMC Genomics. 6:152.
36. Sambrook JG, Russell R, Umrania Y, Edwards YJ, Campbell RD, Elgar G, Clark MS. 2002. Fugu orthologues of human major histocompatibility complex genes: A genome survey. Immunogenetics 54:367-380.
37. Sato A, Dongak R, Hao L, Takezaki N, Shintani S, Aoki T, Klein J. 2006. Mhc class I genes of the cichlid fish Oreochromis niloticus. Immunogenetics 58:917-928.
38. Sato A, Figueroa F, O'hUigin C, Reznick DN, Klein J. 1996. Identification of major histocompatibility complex genes in the guppy, Poecilia reticulata. Immunogenetics 43:38-49.
39. Sato A, Figueroa F, O'hUigin C, Steck N, Klein J. 1998. Cloning of major histocompatibility complex (Mhc) genes from threespine stickleback, Gasterosteus aculeatus. Mol Mar Biol Biotechnol. 7:221-231.
40. Sato A, Klein D, Sultmann H, Figueroa F, O'hUigin C, Klein J. 1997. Class I mhc genes of cichlid fishes: Identification, expression, and polymorphism. Immunogenetics 46:63-72.
41. Sato A, Sultmann H, Mayer WE, Klein J. 2000. Mhc class I gene of African lungfish. Immunogenetics 51:491-495.
42. Schaschl H, Tobler M, Plath M, Penn DJ, Schlupp I. 2008. Polymorphic MHC loci in an asexual fish, the amazon molly (Poecilia formosa; Poeciliidae). Mol Ecol. 17:5220-5230.
43. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W. 2000. PipMaker-a web server for aligning two genomic DNA sequences. Genome Res. 10:577-586.
44. Setiamarga DH, Miya M, Yamanoue Y, Azuma Y, Inoue JG, Ishiguro NB, Mabuchi K, Nishida M. 2009. Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol Lett. 5:812-816.
45. Shiina T, Dijkstra JM, Shimizu S, et al. (15 co-authors). 2005. Interchromosomal duplication of major histocompatibility complex class I regions in rainbow trout (Oncorhynchus mykiss), a species with a presumably recent tetraploid ancestry. Immunogenetics. 56:878-893.
46. Shiina T, Shimizu S, Hosomichi K, Kohara S, Watanabe S, Hanzawa K, Beck S, Kulski JK, Inoko H. 2004. Comparative genomic analysis of two avian (quail and chicken) MHC regions. J Immunol. 172:6751-6763.
47. Shum BP, Guethlein L, Flodin LR, Adkison MA, Hedrick RP, Nehring RB, Stet RJ, Secombes C, Parham P. 2001. Modes of salmonid MHC class I and II evolution differ from the primate paradigm. J Immunol. 166:3297-3308.
48. Siddle HV, Deakin JE, Coggill P, Hart E, Cheng Y, Wong ES, Harrow J, Beck S, Belov K. 2009. MHC-linked and un-linked class I genes in the wallaby. BMC Genomics. 10:310.
49. Srisapoome P, Ohira T, Hirono I, Aoki T. 2004. Genes of the constant regions of functional immunoglobulin heavy chain of Japanese flounder, Paralichthys olivaceus. Immunogenetics 56: 292-300.
50. Stet RJ, Kruiswijk CP, Saeij JP, Wiegertjes GF. 1998. Major histocompatibility genes in cyprinid fishes: Theory and practice. Immunol Rev. 166:301-316.
51. 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.
52. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
53. Tsukamoto K, Hayashi S, Matsuo MY, Nonaka MI, Kondo M, Shima A, Asakawa S, Shimizu N, Nonaka M. 2005. Unprecedented intraspecific diversity of the MHC class I region of a teleost medaka, Oryzias latipes. Immunogenetics 57:420-431.
54. Wang D, Zhong L, Wei Q, Gan X, He S. 2010. Evolution of MHC class I genes in two ancient fish, paddlefish (Polyodon spathula) and Chinese sturgeon (Acipenser sinensis). FEBS Lett. 584:3331-3339.