Identification of chemosensory receptor genes from vertebrate genomes

Methods in Molecular Biology

Volumn 1068, Issue , 2013, Pages 95-105

  Niimura, Yoshihito ^a  

^a TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

Author keywords

Bioinformatics; G protein coupled receptor; Multigene family; Olfactory receptor; Vertebrate; Vomeronasal receptor

Indexed keywords

AMINO ACID;

ANIMAL CELL; ARTICLE; CHEMOSENSORY RECEPTOR GENE; GENE IDENTIFICATION; GENE SEQUENCE; GENOME; MOUSE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OLFACTORY RECEPTOR; ORGANISMS; PHYLOGENETIC TREE; PRIORITY JOURNAL; PSEUDOGENE; RAT; RECEPTOR GENE; STOP CODON; VERTEBRATE; VOMERONASAL ORGAN; VOMERONASAL RECEPTORS TYPE 1; VOMERONASAL RECEPTORS TYPE 2;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; MULTIGENE FAMILY; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, ODORANT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SMELL; VERTEBRATES; VOMERONASAL ORGAN;

EID: 84884200022     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-619-1_7     Document Type: Article

References (30)

1. Nei M, Niimura Y, Nozawa M (2008) The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 9:951-963
2. Niimura Y (2012) Olfactory receptor multigene family in vertebrates: from the viewpoint of evolutionary genomics. Curr Genomics 13:103-114
3. Buck L, Axel R (1991) A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65:175-187
4. Niimura Y, Nei M (2005) Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci USA 102:6039-6044
5. Niimura Y (2009) On the origin and evolution of vertebrate olfactory receptor genes: Comparative genome analysis among 23 chordate species. Genome Biol Evol 1:34-44
6. Dulac C, Axel R (1995) A novel family of genes encoding putative pheromone receptors in mammals. Cell 83:195-206
7. Herrada G, Dulac C (1997) A novel family of putative pheromone receptors in mammals with a topographically organized and sexually dimorphic distribution. Cell 90:763-773
8. Matsunami H, Buck LB (1997) A multigene family encoding a diverse array of putative pheromone receptors in mammals. Cell 90:775-784
9. Ryba NJ, Tirindelli R (1997) A new multigene family of putative pheromone receptors. Neuron 19:371-379
10. Saraiva LR, Korsching SI (2007) A novel olfactory receptor gene family in teleost fish. Genome Res 17:1448-1457
11. Hashiguchi Y, Nishida M (2005) Evolution of vomeronasal-type odorant receptor genes in the zebrafish genome. Gene 362:19-28
12. Niimura Y, Nei M (2007) Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2:e708
13. Hayden S, Bekaert M, Crider TA et al (2010) Ecological adaptation determines functional mammalian olfactory subgenomes. Genome Res 20:1-9
14. Matsui A, Go Y, Niimura Y (2010) Degeneration of olfactory receptor gene repertories in primates: No direct link to full trichromatic vision. Mol Biol Evol 27:1192-1200
15. Grus WE, Shi P, Zhang YP et al (2005) Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals. Proc Natl Acad Sci USA 102:5767-5772
16. Young JM, Kambere M, Trask BJ et al (2005) Divergent V1R repertoires in five species: Amplification in rodents, decimation in primates, and a surprisingly small repertoire in dogs. Genome Res 15:231-240
17. Shi P, Zhang J (2007) Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land. Genome Res 17:166-174
18. Young JM, Massa HF, Hsu L et al (2010) Extreme variability among mammalian V1R gene families. Genome Res 20:10-18
19. Hashiguchi Y, Nishida M (2006) Evolution and origin of vomeronasal-type odorant receptor gene repertoire in fishes. BMC Evol Biol 6:76
20. Young JM, Trask BJ (2007) V2R gene families degenerated in primates, dog and cow, but expanded in opossum. Trends Genet 23:212-215
21. Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
22. Katoh K, Kuma K, Toh H et al (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511-518
23. Takezaki N, Rzhetsky A, Nei M (1995) Phylogenetic test of molecular clock and linearized trees. Mol Biol Evol 12:823-833
24. Eddy SR (2011) Accelerated Profile HMM Searches. PLoS Comput Biol 7:e1002195
25. Birney E, Clamp M, Durbin R (2004) Gene Wise and Genomewise. Genome Res 14:988-995
26. Yang H, Shi P, Zhang YP et al (2005) Composition and evolution of the V2r vomeronasal receptor gene repertoire in mice and rats. Genomics 86:306-315
27. Man O, Gilad Y, Lancet D (2004) Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons. Protein Sci 13:240-254
28. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
29. Go Y, Niimura Y (2008) Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Mol Biol Evol 25:1897-1907
30. Fredriksson R, Lagerström MC, Lundin LG et al (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 63: 1256-1272