Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice

Gene

Volumn 346, Issue , 2005, Pages 13-21

  Niimura, Yoshihito ^a,b   Nei, Masatoshi ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

Author keywords

Birth and death process; Comparative genomics; Genomic cluster; Molecular phylogeny; Tandem gene duplication

Indexed keywords

ARTICLE; CHROMOSOME; COMPARATIVE STUDY; CONTROLLED STUDY; GENE CLUSTER; GENE IDENTIFICATION; GENE LOCATION; GENE NUMBER; GENETIC CONSERVATION; GENETIC ORGANIZATION; GENETIC VARIABILITY; GENOME; GENOME ANALYSIS; GENOMICS; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; MOUSE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OLFACTORY RECEPTOR; PHYLOGENY; PRIORITY JOURNAL; PSEUDOGENE; RECEPTOR GENE; SPECIES DIFFERENCE; UNINDEXED SEQUENCE;

EID: 14744284678     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.09.025     Document Type: Article

References (30)

1. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
2. C. Amadou, R.M. Younger, S. Sims, L.H. Matthews, J. Rogers, A. Kumanovics, A. Ziegler, S. Beck, and K.F. Lindahl Co-duplication of olfactory receptor and MHC class I genes in the mouse major histocompatibility complex Hum. Mol. Genet. 12 2003 3025 3040
3. M. Bulger, J.H. van Doorninck, N. Saitoh, A. Telling, C. Farrell, M.A. Bender, G. Felsenfeld, R. Axel, M. Groudine, and J.H. von Doorninck Conservation of sequence and structure flanking the mouse and human β-globin loci: the β-globin genes are embedded within an array of odorant receptor genes Proc. Natl. Acad. Sci. U. S. A. 96 1999 5129 5134
4. M. Bulger, M.A. Bender, J.H. van Doorninck, B. Wertman, C.M. Farrell, G. Felsenfeld, M. Groudine, and R. Hardison Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse β-globin gene clusters Proc. Natl. Acad. Sci. U. S. A. 97 2000 14560 14565
5. S. Firestein How the olfactory system makes sense of scents Nature 413 2001 211 218
6. G. Glusman, A. Bahar, D. Sharon, Y. Pilpel, J. White, and D. Lancet The olfactory receptor gene superfamily: data mining, classification, and nomenclature Mamm. Genome 11 2000 1016 1023
7. G. Glusman, I. Yanai, I. Rubin, and D. Lancet The complete human olfactory subgenome Genome Res. 11 2001 685 702
8. P.A. Godfrey, B. Malnic, and L.B. Buck The mouse olfactory receptor gene family Proc. Natl. Acad. Sci. U. S. A. 101 2004 2156 2161
9. R. Hoppe, H. Breer, and J. Strotmann Organization and evolutionary relatedness of OR37 olfactory receptor genes in mouse and human Genomics 82 2003 355 364
10. K. Katoh, K. Misawa, K. Kuma, and T. Miyata MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res. 30 2002 3059 3066
11. R.P. Lane, T. Cutforth, J. Young, M. Athanasiou, C. Friedman, L. Rowen, G. Evans, R. Axel, L. Hood, and B.J. Trask Genomic analysis of orthologous mouse and human olfactory receptor loci Proc. Natl. Acad. Sci. U. S. A. 98 2001 7390 7395
12. R.P. Lane, J.C. Roach, I.Y. Lee, C. Boysen, A. Smit, B.J. Trask, and L. Hood Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor α/δ loci Genome Res. 12 2002 81 87
13. M. Lapidot, Y. Pilpel, Y. Gilad, A. Falcovitz, D. Sharon, T. Haaf, and D. Lancet Mouse-human orthology relationships in an olfactory receptor gene cluster Genomics 71 2001 296 306
14. The MHC Sequencing Consortium Complete sequence and gene map of a human major histocompatibility complex Nature 401 1999 921 923
15. P. Mombaerts Genes and ligands for odorant, vomeronasal and taste receptors Nat. Rev., Neurosci. 5 2004 263 278
16. M. Nei Gene duplication and nucleotide substitution in evolution Nature 221 1969 40 42
17. M. Nei, and S. Kumar Molecular Evolution and Phylogenetics 2000 Oxford University Press New York
18. M. Nei, X. Gu, and T. Sitnikova Evolution by the birth-and-death process in multigene families of the vertebrate immune system Proc. Natl. Acad. Sci. U. S. A. 94 1997 7799 7806
19. T. Newman, and B.J. Trask Complex evolution of 7E olfactory receptor genes in segmental duplications Genome Res. 13 2003 781 793
20. Y. Niimura, and M. Nei Evolution of olfactory receptor genes in the human genome Proc. Natl. Acad. Sci. U. S. A. 100 2003 12235 12240
21. N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
22. D. Sharon, G. Glusman, Y. Pilpel, M. Khen, F. Gruetzner, T. Haaf, and D. Lancet Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes Genomics 61 1999 24 36
23. G.P. Smith Unequal crossover and the evolution of multigene families Cold Spring Harbor Symp. Quant. Biol. 38 1974 507 513
24. N. Takezaki, A. Rzhetsky, and M. Nei Phylogenetic test of the molecular clock and linearized trees Mol. Biol. Evol. 12 1995 823 833
25. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
26. J.M. Young, C. Friedman, E.M. Williams, J.A. Ross, L. Tonnes-Priddy, and B.J. Trask Different evolutionary processes shaped the mouse and human olfactory receptor gene families Hum. Mol. Genet. 11 2002 535 546
27. R.M. Younger, C. Amadou, G. Bethel, A. Ehlers, K.F. Lindahl, S. Forbes, R. Horton, S. Milne, A.J. Mungall, J. Trowsdale, A. Volz, A. Ziegler, and S. Beck Characterization of clustered MHC-linked olfactory receptor genes in human and mouse Genome Res. 11 2001 519 530
28. X. Zhang, and S. Firestein The olfactory receptor gene superfamily of the mouse Nat. Neurosci. 5 2002 124 133
29. X. Zhang, I. Rodriguez, P. Mombaerts, and S. Firestein Odorant and vomeronasal receptor genes in two mouse genome assemblies Genomics 83 2004 802 811
30. Zozulya, S., Echeverri, F., Nguyen, T., 2001. The human olfactory receptor repertoire. Genome Biol. 2, research0018.1-0018.12.