Evolution of the proto-MHC ancestral region: More evidence for the plesiomorphic organisation of human chromosome 9q34 region

Immunogenetics

Volumn 55, Issue 7, 2003, Pages 429-436

  Vienne, Alexandre ^a   Shiina, Takashi ^b   Abi Rached, Laurent ^c   Danchin, Etienne ^a   Vitiello, Verane ^a   Cartault, François ^d   Inoko, Hidetoshi ^b   Pontarotti, Pierre ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

^b TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d Centre Hospitalier Departemental Felix Guyon   (France)

Author keywords

Amphioxus; En bloc duplication; MHC; Paralogous region; Plesiomorphy

Indexed keywords

GLUCOSYLTRANSFERASE; MAJOR HISTOCOMPATIBILITY ANTIGEN; SIALIDASE;

AMINO ACID SEQUENCE; ARTICLE; BRANCHIOSTOMA FLORIDAE; CHORDATA; CHROMOSOME 9Q; CHROMOSOME DUPLICATION; CONTROLLED STUDY; COSMID; DNA LIBRARY; GENE IDENTIFICATION; GENE LOCATION; GENETIC VARIABILITY; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PHYLOGENY; PLESIOMORPHY; PRIORITY JOURNAL;

ANIMALS; CHROMOSOMES, HUMAN, PAIR 9; EVOLUTION, MOLECULAR; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

BRANCHIOSTOMA; BRANCHIOSTOMA FLORIDAE; BRANCHIOSTOMA LANCEOLATUM; CEPHALOCHORDATA; CHORDATA; MYA; VERTEBRATA;

EID: 0242468325     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00251-003-0601-x     Document Type: Article

References (20)

1. Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H (2002) Evidence of en bloc duplication in vertebrate genomes. Nature Genetics 31:100-105
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam Protein Families Database. Nucleic Acids Res 30:276-280
4. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291:1289-1292
5. Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2:292-301
6. Doolittle RF (1995) The multiplicity of domains in proteins. Annu Rev Biochem 6:287-314
7. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
8. Gu X, Wang Y, Gu J (2002) Age distribution of human gene families shows significant roles of both large-and small-scale duplications in vertebrate evolution. Nat Genet 31:205-209
9. Kasahara M, Hayashi M, Tanaka K, Inoko H, Sugaya K, Ikemura T, Ishibashi T (1996) Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex. Proc Natl Acad Sci USA 93:9096-9101
10. Katsanis M, Fitzgibbon J, Fisher EMC (1996) Paralogy mapping: identification of a region in the human MHC triplicated onto human chromosomes 1 and 9 allows the prediction and isolation of novel PBX and NOTCH loci. Genomics 35:101-108
11. Ku HM, Vision T, Liu J, Tanksley SD (2000) Comparing sequenced segments of tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of syntheny. Proc Natl Acad Sci USA 97:9121-9126
12. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17:1244-1245
13. Lundin LG (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16:1-19
14. Minguillón C, Ferner DEK, Cebrián C, Garcia- Fernàndez J (2002) Gene duplications in the prototypical cephalochordate amphioxus. Gene 287:121-128
15. Philippe H (1993) MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 21:5264-5272
16. Shiina T, Ando A, Suto Y, Kasai F, Shigenari A, Takishima N, Kikkawa E, Iwata K, Kuwano Y, Kitamura Y, Matsuzawa Y, Sano K, Nogami M, Kawata H, Li S, Fukuzumi Y, Yamazaki M, Tashiro H, Tamiya G, Kohda A, Okumura K, Ikemura T, Soeda E, Mizuki N, Kimura M, Bahram S, Inoko H (2001) Genomic anatomy of a premier major histocompatibility complex paralogous region on chromosome 1q21-q22. Genome Res 11:789-802
17. Strimmer K, Haeseler A (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969
18. Swofford DL (2000) PAUP *. Phylogenetic Analysis Using Parsimony (* and other Methods), version 4. Sinauer, Sunderland, Massachusetts
19. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
20. Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P (2002) Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298:149-159