Identification of Olfactory Receptor Genes from Mammalian Genome Sequences

  • Yoshihito Niimura
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1003)

Abstract

Olfaction is essential for the survival of mammals. Diverse odorant molecules in the environment are detected by olfactory receptors (ORs) expressed in the olfactory epithelium of the nasal cavity. In general, mammalian genomes harbor ∼1,000 OR genes, which form the largest multigene family in mammals. The recent advances in genome sequencing technology have enabled us to computationally identify nearly complete repertoires of OR genes from various organisms. Such studies have revealed that the numbers of OR genes are highly variable among organisms depending on their living environments.

Because OR genes are intronless, it is possible to find all OR genes by conducting homology searches against the genome sequences using known OR genes as queries. However, some caution is necessary during the process of extracting intact coding sequences of OR genes and distinguishing among OR and non-OR genes. Presented here is a description of bioinformatics methods to identify the entire OR gene repertoires from mammalian genome sequences.

Key words

Olfactory receptor Multigene family Bioinformatics Mammalian genome G-protein coupled receptor 

References

  1. 1.
    Niimura Y (2009) Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents. Hum Genomics 4:107–118PubMedCrossRefGoogle Scholar
  2. 2.
    Niimura Y (2012) Olfactory receptor multigene family in vertebrates: from the viewpoint of evolutionary genomics. Curr Genomics 13:103–114PubMedCrossRefGoogle Scholar
  3. 3.
    Buck L, Axel R (1991) A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65:175–187PubMedCrossRefGoogle Scholar
  4. 4.
    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 63:1256–1272PubMedCrossRefGoogle Scholar
  5. 5.
    Young JM, Shykind BM, Lane RP et al (2003) Odorant receptor expressed sequence tags demonstrate olfactory expression of over 400 genes, extensive alternate splicing and unequal expression levels. Genome Biol 4:R71PubMedCrossRefGoogle Scholar
  6. 6.
    Niimura Y, Nei M (2005) Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci USA 102:6039–6044PubMedCrossRefGoogle Scholar
  7. 7.
    Niimura Y (2009) On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species. Genome Biol Evol 1:34–44PubMedCrossRefGoogle Scholar
  8. 8.
    Glusman G, Bahar A, Sharon D et al (2000) The olfactory receptor gene superfamily: data mining, classification, and nomenclature. Mamm Genome 11:1016–1023PubMedCrossRefGoogle Scholar
  9. 9.
    Nei M, Niimura Y, Nozawa M (2008) The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 9:951–963PubMedCrossRefGoogle Scholar
  10. 10.
    Niimura Y, Nei M (2003) Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci USA 100:12235–12240PubMedCrossRefGoogle Scholar
  11. 11.
    Niimura Y, Nei M (2005) Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene 346:13–21PubMedCrossRefGoogle Scholar
  12. 12.
    Niimura Y, Nei M (2005) Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages. Gene 346:23–28PubMedCrossRefGoogle Scholar
  13. 13.
    Niimura Y, Nei M (2007) Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2:e708PubMedCrossRefGoogle Scholar
  14. 14.
    Go Y, Niimura Y (2008) Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Mol Biol Evol 25:1897–1907PubMedCrossRefGoogle Scholar
  15. 15.
    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 27:1192–1200PubMedCrossRefGoogle Scholar
  16. 16.
    Crasto C, Marenco L, Miller PL et al (2002) Olfactory receptor database: a metadata-driven automated population from sources of gene and protein sequences. Nucleic Acids Res 30:354–360PubMedCrossRefGoogle Scholar
  17. 17.
    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 25:3389–3402PubMedCrossRefGoogle Scholar
  18. 18.
    Katoh K, Kuma K, Toh H et al (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511–518PubMedCrossRefGoogle Scholar
  19. 19.
    Man O, Gilad Y, Lancet D (2004) Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons. Protein Sci 13:240–254PubMedCrossRefGoogle Scholar
  20. 20.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  21. 21.
    Takezaki N, Rzhetsky A, Nei M (1995) Phylogenetic test of molecular clock and linearized trees. Mol Biol Evol 12:823–833PubMedGoogle Scholar
  22. 22.
    Crooks GE, Hon G, Chandonia JM et al (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Yoshihito Niimura
    • 1
  1. 1.Department of Bioinformatics, Medical Research InstituteTokyo Medical and Dental UniversityTokyoJapan

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