Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes
<p>Abstract</p> <p>Background</p> <p>Routine trichromatic color vision is a characteristic feature of catarrhines (humans, apes and Old World monkeys). This is enabled by L and M opsin genes arrayed on the X chromosome and an autosomal S opsin gene. In non-human catarrh...
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| Format: | Article |
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BMC
2011-10-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/11/312 |
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| author | Siriaroonrat Boripat Malaivijitnond Suchinda Perwitasari-Farajallah Dyah Suryobroto Bambang Katsumura Takafumi Mikami Akichika Hiwatashi Tomohide Oota Hiroki Goto Shunji Kawamura Shoji |
| author_facet | Siriaroonrat Boripat Malaivijitnond Suchinda Perwitasari-Farajallah Dyah Suryobroto Bambang Katsumura Takafumi Mikami Akichika Hiwatashi Tomohide Oota Hiroki Goto Shunji Kawamura Shoji |
| author_sort | Siriaroonrat Boripat |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Routine trichromatic color vision is a characteristic feature of catarrhines (humans, apes and Old World monkeys). This is enabled by L and M opsin genes arrayed on the X chromosome and an autosomal S opsin gene. In non-human catarrhines, genetic variation affecting the color vision phenotype is reported to be absent or rare in both L and M opsin genes, despite the suggestion that gene conversion has homogenized the two genes. However, nucleotide variation of both introns and exons among catarrhines has only been examined in detail for the L opsin gene of humans and chimpanzees. In the present study, we examined the nucleotide variation of gibbon (Catarrhini, Hylobatidae) L and M opsin genes. Specifically, we focused on the 3.6~3.9-kb region that encompasses the centrally located exon 3 through exon 5, which encode the amino acid sites functional for the spectral tuning of the genes.</p> <p>Results</p> <p>Among 152 individuals representing three genera (<it>Hylobates</it>, <it>Nomascus </it>and <it>Symphalangus</it>), all had both L and M opsin genes and no L/M hybrid genes. Among 94 individuals subjected to the detailed DNA sequencing, the nucleotide divergence between L and M opsin genes in the exons was significantly higher than the divergence in introns in each species. The ratio of the inter-LM divergence to the intra-L/M polymorphism was significantly lower in the introns than that in synonymous sites. When we reconstructed the phylogenetic tree using the exon sequences, the L/M gene duplication was placed in the common ancestor of catarrhines, whereas when intron sequences were used, the gene duplications appeared multiple times in different species. Using the GENECONV program, we also detected that tracts of gene conversions between L and M opsin genes occurred mostly within the intron regions.</p> <p>Conclusions</p> <p>These results indicate the historical accumulation of gene conversions between L and M opsin genes in the introns in gibbons. Our study provides further support for the homogenizing role of gene conversion between the L and M opsin genes and for the purifying selection against such homogenization in the central exons to maintain the spectral difference between L and M opsins in non-human catarrhines.</p> |
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| institution | Directory Open Access Journal |
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| last_indexed | 2024-04-11T15:02:03Z |
| publishDate | 2011-10-01 |
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| spelling | doaj.art-c07b5066cf7640239be0b834f520e3b12022-12-22T04:16:57ZengBMCBMC Evolutionary Biology1471-21482011-10-0111131210.1186/1471-2148-11-312Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genesSiriaroonrat BoripatMalaivijitnond SuchindaPerwitasari-Farajallah DyahSuryobroto BambangKatsumura TakafumiMikami AkichikaHiwatashi TomohideOota HirokiGoto ShunjiKawamura Shoji<p>Abstract</p> <p>Background</p> <p>Routine trichromatic color vision is a characteristic feature of catarrhines (humans, apes and Old World monkeys). This is enabled by L and M opsin genes arrayed on the X chromosome and an autosomal S opsin gene. In non-human catarrhines, genetic variation affecting the color vision phenotype is reported to be absent or rare in both L and M opsin genes, despite the suggestion that gene conversion has homogenized the two genes. However, nucleotide variation of both introns and exons among catarrhines has only been examined in detail for the L opsin gene of humans and chimpanzees. In the present study, we examined the nucleotide variation of gibbon (Catarrhini, Hylobatidae) L and M opsin genes. Specifically, we focused on the 3.6~3.9-kb region that encompasses the centrally located exon 3 through exon 5, which encode the amino acid sites functional for the spectral tuning of the genes.</p> <p>Results</p> <p>Among 152 individuals representing three genera (<it>Hylobates</it>, <it>Nomascus </it>and <it>Symphalangus</it>), all had both L and M opsin genes and no L/M hybrid genes. Among 94 individuals subjected to the detailed DNA sequencing, the nucleotide divergence between L and M opsin genes in the exons was significantly higher than the divergence in introns in each species. The ratio of the inter-LM divergence to the intra-L/M polymorphism was significantly lower in the introns than that in synonymous sites. When we reconstructed the phylogenetic tree using the exon sequences, the L/M gene duplication was placed in the common ancestor of catarrhines, whereas when intron sequences were used, the gene duplications appeared multiple times in different species. Using the GENECONV program, we also detected that tracts of gene conversions between L and M opsin genes occurred mostly within the intron regions.</p> <p>Conclusions</p> <p>These results indicate the historical accumulation of gene conversions between L and M opsin genes in the introns in gibbons. Our study provides further support for the homogenizing role of gene conversion between the L and M opsin genes and for the purifying selection against such homogenization in the central exons to maintain the spectral difference between L and M opsins in non-human catarrhines.</p>http://www.biomedcentral.com/1471-2148/11/312 |
| spellingShingle | Siriaroonrat Boripat Malaivijitnond Suchinda Perwitasari-Farajallah Dyah Suryobroto Bambang Katsumura Takafumi Mikami Akichika Hiwatashi Tomohide Oota Hiroki Goto Shunji Kawamura Shoji Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes BMC Evolutionary Biology |
| title | Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes |
| title_full | Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes |
| title_fullStr | Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes |
| title_full_unstemmed | Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes |
| title_short | Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes |
| title_sort | gene conversion and purifying selection shape nucleotide variation in gibbon l m opsin genes |
| url | http://www.biomedcentral.com/1471-2148/11/312 |
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