The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation

We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number ( N ), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsi...

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Published in	Scientific reports Vol. 7; no. 1; pp. 15568 - 13
Main Authors	Lin, Jinn-Jy, Wang, Feng-Yu, Li, Wen-Hsiung, Wang, Tzi-Yuan
Format	Journal Article
Language	English
Published	London Nature Publishing Group UK 14.11.2017 Nature Publishing Group
Subjects	631/114/2184 631/181/735 Animals Copy number Ecological adaptation Evolution Evolution, Molecular Evolutionary genetics Fishes - genetics Genes Genome - genetics Genomes Humanities and Social Sciences Metagenomics multidisciplinary Opsins - classification Opsins - genetics Phylogeny Rhodopsin Rod Opsins - classification Rod Opsins - genetics Science Science (multidisciplinary) Synteny Synteny - genetics
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ISSN	2045-2322 2045-2322
DOI	10.1038/s41598-017-15868-7

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Abstract	We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number ( N ), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.
AbstractList	We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number ( N ), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution. We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution. We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.
ArticleNumber	15568
Author	Li, Wen-Hsiung Lin, Jinn-Jy Wang, Tzi-Yuan Wang, Feng-Yu
Author_xml	– sequence: 1 givenname: Jinn-Jy surname: Lin fullname: Lin, Jinn-Jy organization: Institute of Molecular and Cellular Biology, National Tsing Hua University, Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Nankang, Biodiversity Research Center, Academia Sinica, Nankang – sequence: 2 givenname: Feng-Yu surname: Wang fullname: Wang, Feng-Yu organization: Taiwan Ocean Research Institute, National Applied Research Laboratories – sequence: 3 givenname: Wen-Hsiung surname: Li fullname: Li, Wen-Hsiung email: whli@sinica.edu.tw organization: Institute of Molecular and Cellular Biology, National Tsing Hua University, Biodiversity Research Center, Academia Sinica, Nankang, Department of Ecology and Evolution, University of Chicago – sequence: 4 givenname: Tzi-Yuan surname: Wang fullname: Wang, Tzi-Yuan email: tziyuan@gmail.com organization: Biodiversity Research Center, Academia Sinica, Nankang
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/29138475$$D View this record in MEDLINE/PubMed
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Snippet	We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we...
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StartPage	15568
SubjectTerms	631/114/2184 631/181/735 Animals Copy number Ecological adaptation Evolution Evolution, Molecular Evolutionary genetics Fishes - genetics Genes Genome - genetics Genomes Humanities and Social Sciences Metagenomics multidisciplinary Opsins - classification Opsins - genetics Phylogeny Rhodopsin Rod Opsins - classification Rod Opsins - genetics Science Science (multidisciplinary) Synteny Synteny - genetics
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Title	The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation
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