Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
Sci Rep. 2017 Nov 14;7(1):15568. doi: 10.1038/s41598-017-15868-7.
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.
我们研究了 59 种硬骨鱼类基因组中视蛋白基因的进化。我们在每个基因组中鉴定了视蛋白基因和相邻基因（基因同线性）。然后，我们推断了在进化过程中沿每个系统发育分支的基因拷贝数（N）、基因同线性和调谐位点的变化。Exorh（视杆蛋白基因）在 56 个基因组中被保留。Rh1，无内含子的视杆蛋白基因，最初出现在祖先的肉鳍鱼中，N 通过硬骨鱼特有的全基因组复制增加到 2，但随后在新鳍鱼的祖先中减少到 1。对于视锥蛋白基因，视紫红质样（Rh2）和长波敏感（LWS）基因在物种间的 N 变化很大，范围分别为 0 到 5 和 0 到 4。两个短波敏感基因 SWS1 和 SWS2 分别在 23 和 6 个物种中丢失。涉及 LWS、SWS2 和 Rh2 的基因同线性发生了复杂的变化，而其他视蛋白基因同线性的进化则要简单得多。讨论了不同生活环境下调谐位点的进化适应。我们的研究提供了硬骨鱼进化过程中视蛋白基因获得和丢失、基因同线性变化和调谐位点变化的详细视图。
