非视觉视蛋白是在许多动物的眼睛和其他组织中表达的跨膜蛋白。当与光敏发色团配对时,非视觉视蛋白形成涉及各种非视觉的光色素,光检测功能,包括昼夜节律调节,寻求光的行为,和季节性反应。在这里,我们研究了无双两栖动物(青蛙和蟾蜍)中非视觉视蛋白基因的分子进化。我们测试了几种进化假设,包括由于夜间祖先而导致的非视觉视蛋白的预测损失,以及由于不同无神经生态的环境光变化而导致的非视觉视蛋白的潜在功能差异。使用81个物种的全眼转录组,结合基因组,多组织转录组,并独立注释了来自另外21个物种的基因,我们确定哪些非视觉视蛋白存在于无性系基因组中,以及那些也在眼睛中表达的视蛋白,比较基因之间的选择性约束,并通过比较离散生态类之间的选择来检验潜在的适应性进化。在基因组层面,我们恢复了所有18种祖先脊椎动物的非视觉视蛋白,表明在祖先的夜间四足动物中,无神经显示出最低的视蛋白基因丢失量。我们一致地发现了14种非视觉视蛋白在无脑眼中的表达,并在这些基因的子集中检测到了阳性选择。我们还发现,在不同活动期的青蛙中,作用于非视觉视蛋白的选择性约束发生了变化,栖息地,分布,生活史,和瞳孔形状,这可能反映了功能适应。尽管许多非视觉视蛋白仍然知之甚少,这些发现提供了对这些基因在无性系中的多样性和进化的见解,填补了我们对脊椎动物视蛋白的理解的重要空白,并为未来研究它们跨分类群的功能进化奠定了基础。
Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.