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

Jinn-Jy Lin,Wen-Hsiung Li,Feng-Yu Wang,Tzi-Yuan Wang

doi:10.1038/s41598-017-15868-7

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.

Highlights

Visual perception is important for an animal because it conveys the color, shape, size and movement of its surrounding objects
Two short-wavelength sensitive (SWS1 and SWS2), one middle-wavelength sensitive (Rh2), and one long-wavelength sensitive (LWS) opsin genes are responsible for photopic vision
In addition to the substitution events reported in the literature[37], we identified more substitutions in the LWS phylogenetic tree (Fig. 7)

Summary

Introduction

Visual perception is important for an animal because it conveys the color, shape, size and movement of its surrounding objects. The visual capability of an animal depends on the opsin genes it possesses. Phototransduction occurs via the interaction between opsin proteins and vitamin A-derived chromophore[2]. Two short-wavelength sensitive (SWS1 and SWS2), one middle-wavelength sensitive (Rh2), and one long-wavelength sensitive (LWS) opsin genes are responsible for photopic vision. The diversity of habitats in the aqueous environment is a driving force of the evolution of opsin genes in fishes. Tandem duplication and whole genome duplication (WGD) have played important roles in the evolution of opsin genes in fishes[16,17]. It was hypothesized that the five opsin families were derived from duplication events in the genome of the common ancestor of vertebrates[16,17]. The evolutionary dynamics of opsin gene syntenies was not investigated in detail

Methods

Results

Conclusion