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.

视觉是维系生物体生存的关键感知能力，其视觉敏感性受环境因素强烈塑造。部分具有冈瓦纳起源（Gondwanan）的淡水鱼类，其分布范围涵盖包括亚马孙河在内的南美洲河流，以及非洲的河流与湖泊。这些环境差异极大的生境，大概率要求这类物种分别适应浑浊与清澈两类水环境。本研究针对亚马孙与非洲慈鲷鱼类（cichlid）的视觉系统分子基础展开对比分析。我们采用基因组与视网膜转录组（retinal transcriptome）的下一代测序（next generation sequencing）技术，对3种亚马孙慈鲷物种进行研究。基因组组装结果显示，该类鱼类拥有6类视锥视蛋白（cone opsin：SWS1、SWS2B、SWS2A、RH2B、RH2A、LWS）与1类视杆视蛋白（rod opsin：RH1）。不过不同物种间这些基因的功能存在差异，不同物种携带的假基因（pseudogene）类型各不相同。我们的研究结果佐证了一项此前的发现：RH2A基因重复（gene duplication）事件在两类慈鲷类群中均有发生，但该事件之后大概率伴随了基因转换（gene conversion）过程。转录组分析表明，亚马孙慈鲷主要表达3类视蛋白（SWS2A、RH2A与LWS），这一表达模式很可能与亚马孙流域以长波长光为主的光照环境高度适配。此外，氨基酸序列分析显示，短波长敏感基因（SWS2B、SWS2A）可能处于选择压力之下，以调整其光谱特性，适配更长波长的视觉环境。我们的研究结果与‘敏感性假说 (sensitivity hypothesis)’的理论相符，该假说提出光照环境会驱动视觉系统的适应性演化。亚马孙慈鲷的视觉系统大概率通过基因表达调控、基因丢失，以及视蛋白序列的光谱微调这三种机制实现适应性演化。这类适应性演化机制可能同样广泛存在于亚马孙鱼类类群中。