Characterization of Squamate Olfactory Receptor Genes and Their Transcripts by the High-Throughput Sequencing Approach

Yuki Dehara, Yasuyuki Hashiguchi, Kazumi Matsubara, Tokuma Yanai, Masahito Kubo, Yoshinori Kumazawa

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    Abstract

    The olfactory receptor (OR) genes represent the largest multigene family in the genome of terrestrial vertebrates. Here, the high-throughput next-generation sequencing (NGS) approach was applied to characterization of OR gene repertoires in the green anole lizard Anolis carolinensis and the Japanese four-lined ratsnake Elaphe quadrivirgata. Tagged polymerase chain reaction (PCR) products amplified from either genomic DNA or cDNA of the two species were used for parallel pyrosequencing, assembling, and screening for errors in PCR and pyrosequencing. Starting from the lizard genomic DNA, we accurately identified 56 of 136 OR genes that were identified from its draft genome sequence. These recovered genes were broadly distributed in the phylogenetic tree of vertebrate OR genes without severe biases toward particular OR families. Ninety-six OR genes were identified from the ratsnake genomic DNA, implying that the snake has more OR gene loci than the anole lizard in response to an increased need for the acuity of olfaction. This view is supported by the estimated number of OR genes in the Burmese python’s draft genome (;280), although squamates may generally have fewer OR genes than terrestrial mammals and amphibians. The OR gene repertoire of the python seems unique in that many class I OR genes are retained. The NGS approach also allowed us to identify candidates of highly expressed and silent OR gene copies in the lizard’s olfactory epithelium. The approach will facilitate efficient and parallel characterization of considerable unbiased proportions of multigene family members and their transcripts from nonmodel organisms.
    Original languageEnglish
    Pages (from-to)602-616
    Number of pages15
    JournalGenome Biology and Evolution
    Volume4
    DOIs
    Publication statusPublished - 2012

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    Odorant Receptors
    olfactory receptors
    Squamata
    gene
    Genes
    Lizards
    genes
    lizard
    Boidae
    Anolis carolinensis
    lizards
    Python
    genomics
    genome
    Genome
    Multigene Family
    multigene family
    DNA
    polymerase chain reaction
    Vertebrates

    Cite this

    Dehara, Yuki ; Hashiguchi, Yasuyuki ; Matsubara, Kazumi ; Yanai, Tokuma ; Kubo, Masahito ; Kumazawa, Yoshinori. / Characterization of Squamate Olfactory Receptor Genes and Their Transcripts by the High-Throughput Sequencing Approach. In: Genome Biology and Evolution. 2012 ; Vol. 4. pp. 602-616.
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    Characterization of Squamate Olfactory Receptor Genes and Their Transcripts by the High-Throughput Sequencing Approach. / Dehara, Yuki; Hashiguchi, Yasuyuki; Matsubara, Kazumi; Yanai, Tokuma; Kubo, Masahito; Kumazawa, Yoshinori.

    In: Genome Biology and Evolution, Vol. 4, 2012, p. 602-616.

    Research output: Contribution to journalArticle

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    AB - The olfactory receptor (OR) genes represent the largest multigene family in the genome of terrestrial vertebrates. Here, the high-throughput next-generation sequencing (NGS) approach was applied to characterization of OR gene repertoires in the green anole lizard Anolis carolinensis and the Japanese four-lined ratsnake Elaphe quadrivirgata. Tagged polymerase chain reaction (PCR) products amplified from either genomic DNA or cDNA of the two species were used for parallel pyrosequencing, assembling, and screening for errors in PCR and pyrosequencing. Starting from the lizard genomic DNA, we accurately identified 56 of 136 OR genes that were identified from its draft genome sequence. These recovered genes were broadly distributed in the phylogenetic tree of vertebrate OR genes without severe biases toward particular OR families. Ninety-six OR genes were identified from the ratsnake genomic DNA, implying that the snake has more OR gene loci than the anole lizard in response to an increased need for the acuity of olfaction. This view is supported by the estimated number of OR genes in the Burmese python’s draft genome (;280), although squamates may generally have fewer OR genes than terrestrial mammals and amphibians. The OR gene repertoire of the python seems unique in that many class I OR genes are retained. The NGS approach also allowed us to identify candidates of highly expressed and silent OR gene copies in the lizard’s olfactory epithelium. The approach will facilitate efficient and parallel characterization of considerable unbiased proportions of multigene family members and their transcripts from nonmodel organisms.

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