Data from: The opsin genes of Amazonian cichlids

Vision is a critical sense for organismal survival with visual sensitivities strongly shaped by the environment. Some freshwater fishes with a Gondwanan origin are distributed in both South American rivers including the Amazon, as well as African rivers and lakes. These different habitats likely required adaptations to murky and clear environments. In this study, we compare the molecular basis of Amazonian and African cichlid fishes’ visual systems. We used next generation sequencing of genomes and retinal transcriptomes to examine three Amazonian cichlid species. Genome assemblies revealed six cone opsin classes (SWS1, SWS2B, SWS2A, RH2B, RH2A, LWS) and rod opsin (RH1). However, the functionality of these genes varies across species with different pseudogenes found in different species. Our results support evidence of an RH2A gene duplication event that is shared across both cichlid groups, but which was probably followed by gene conversion. Transcriptome analyses show that Amazonian species mainly express three opsin classes (SWS2A, RH2A and LWS) which likely are a good match to the long wavelength oriented light environment of the Amazon basin. Furthermore, analysis of amino acid sequences suggest that the short wavelength sensitive genes (SWS2B, SWS2A) may be under selective pressures in order to shift their spectral properties to a longer wavelength visual palette. Our results agree with the ‘sensitivity hypothesis’ where the light environment causes visual adaptation. Amazonian cichlid visual systems are likely adapting through gene expression, gene loss, and possibly spectral tuning of opsin sequences. Such mechanisms may be shared across the Amazonian fish fauna.

视觉是生物体生存的核心感知能力，其视觉敏感度受环境因素的强烈塑造。部分起源于冈瓦纳大陆（Gondwanan）的淡水鱼类，不仅分布于包括亚马逊河在内的南美洲水系，同时也栖息于非洲的河流与湖泊中。这些迥异的生境很可能要求鱼类分别适应浑浊与清澈两种水环境。本研究针对亚马逊慈鲷与非洲慈鲷的视觉系统分子基础展开对比分析。我们通过基因组与视网膜转录组（retinal transcriptome）的下一代测序技术，对3种亚马逊慈鲷物种进行了研究。基因组组装结果显示，慈鲷拥有6种视锥视蛋白（cone opsin）亚型：SWS1、SWS2B、SWS2A、RH2B、RH2A、LWS，以及1种视杆视蛋白（rod opsin）RH1。但这些基因的功能在不同物种间存在差异，不同物种中均存在各自的假基因（pseudogene）。本研究结果佐证了RH2A基因复制（gene duplication）事件存在的证据：该事件在两类慈鲷类群中均有发生，且后续大概率伴随了基因转换（gene conversion）过程。转录组分析显示，亚马逊慈鲷主要表达3种视蛋白亚型：SWS2A、RH2A与LWS，这一表达模式很可能与亚马逊流域以长波长光为主的光照环境高度适配。此外，氨基酸序列分析表明，短波长敏感型视蛋白基因（SWS2B、SWS2A）可能处于选择压力之下，以调整其光谱特性，适配更偏向长波长的视觉环境。本研究结果与“敏感度假说（sensitivity hypothesis）”相符：光照环境会驱动视觉系统产生适应性演化。亚马逊慈鲷的视觉系统很可能通过基因表达调控、基因丢失，以及视蛋白序列的光谱微调这三种途径实现适应性演化。这类演化机制或许同样适用于亚马逊鱼类群落。