Policarpo Maxime, Fogg Lily G, Cortesi Fabio, Salzburger Walter
Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
School of the Environment, The University of Queensland, Brisbane 4072, Australia.
Genome Biol Evol. 2025 Jul 3;17(7). doi: 10.1093/gbe/evaf129.
Photoreception-the detection of light for image formation (vision) as well as for nonimage-forming purposes (circadian regulation and DNA repair)-is critical to the survival of most animals. In vertebrates, photoreception is mediated by opsin proteins, which are classified, according to their function, into visual and nonvisual opsins. Here, we provide the most comprehensive study to date on the evolution of the opsin gene family in the largest class of vertebrates, actinopterygians, with a particular focus on the understudied nonvisual opsins. Based on an in-depth analysis of 535 high-quality genomes, we document great variation in gene numbers in the different opsin gene subfamilies across ray-finned fishes and show that visual opsins are more prone to duplications and losses than nonvisual opsins. We provide evidence that visual and nonvisual opsins coevolve in ray-finned fishes, both in terms of copy numbers and selective pressures acting on their coding sequences, probably in response to the different photic environments they inhabit. Species that live in dim light or in the dark (such as in caves or the deep sea) had reduced visual and nonvisual opsin gene repertoires, while polar species feature accelerated evolution in both. Fishes that rely on electroreception show a slight reduction in the number of visual and nonvisual opsin genes and accelerated evolution of the remaining genes. We further found that genes of the phototransduction cascade coevolve with opsins. Finally, the finding that nonvisual opsins are mainly expressed in the testes and ovaries (after the eyes) supports a function in gamete biology.
光感受——检测光线以形成图像（视觉）以及用于非图像形成目的（昼夜节律调节和DNA修复）——对大多数动物的生存至关重要。在脊椎动物中，光感受由视蛋白介导，视蛋白根据其功能可分为视觉视蛋白和非视觉视蛋白。在此，我们提供了迄今为止关于硬骨鱼纲（最大的脊椎动物类群）中视蛋白基因家族进化的最全面研究，特别关注研究较少的非视觉视蛋白。基于对535个高质量基因组的深入分析，我们记录了辐鳍鱼类不同视蛋白基因亚家族中基因数量的巨大差异，并表明视觉视蛋白比非视觉视蛋白更容易发生复制和丢失。我们提供的证据表明，在辐鳍鱼类中，视觉视蛋白和非视觉视蛋白在拷贝数和作用于其编码序列的选择压力方面共同进化，这可能是对它们所栖息的不同光环境的响应。生活在弱光或黑暗环境中的物种（如洞穴或深海中的物种）视觉和非视觉视蛋白基因库减少，而极地物种在这两方面都有加速进化。依赖电感受的鱼类视觉和非视觉视蛋白基因数量略有减少，其余基因加速进化。我们还发现光转导级联反应的基因与视蛋白共同进化。最后，非视觉视蛋白主要在睾丸和卵巢（仅次于眼睛）中表达这一发现支持了其在配子生物学中的功能。
