Vertebrates use cone cells in the retina for colour vision and rod cells to see in dim light. Many deep-sea fishes have adapted to their environment to have only rod cells in the retina, while both rod and cone genes are still preserved in their genomes. As deep-sea fish larvae start their lives in the shallow, and only later submerge to the depth, they have to cope with diverse environmental conditions during ontogeny. Using a comparative transcriptomic approach in 20 deep-sea fish species from eight teleost orders, we report on a developmental cone-to-rod switch. While adults mostly rely on rod opsin (RH1) for vision in dim light, larvae almost exclusively express middle-wavelength-sensitive (“green”) cone opsins (RH2) in their retinas. The phototransduction cascade genes follow a similar ontogenetic pattern of cone-followed by rod-specific gene expression in most species, except for the pearleye and sabretooth (Aulopiformes), in which the cone cascade remains dominant throughout development. By inspecting the whole genomes of five deep-sea species (four of them sequenced within this study: Idiacanthus fasciola, Chauliodus sloani; Stomiiformes; Coccorella atlantica, and Scopelarchus michaelsarsi; Aulopiformes), we found that deep-sea fish possess one or two copies of the rod RH1 opsin gene, and up to seven copies of the cone RH2 opsin genes in their genomes, while other cone opsin classes have been mostly lost. Our findings hence provide molecular evidence for a limited opsin gene repertoire and a conserved vertebrate pattern whereby cone photoreceptors develop first and rod photoreceptors are added only at later developmental stages.

中文翻译：

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视觉基因表达揭示了深海鱼类从锥体到杆体的发育进程

脊椎动物使用视网膜中的视锥细胞进行色觉，使用杆状细胞在昏暗的光线下看东西。许多深海鱼类已经适应了它们的环境，在视网膜中只有杆状细胞，而杆状和锥状基因仍然保留在它们的基因组中。由于深海鱼幼虫在浅水区开始生活，然后才潜入深海，因此它们在个体发育过程中必须应对各种环境条件。使用来自八个硬骨目的 20 种深海鱼类的比较转录组学方法，我们报告了发育中的锥杆转换。虽然成虫在昏暗的光线下主要依靠杆状视蛋白 ( RH1 ) 获得视觉，但幼虫几乎只表达对中波长敏感（“绿色”）的视锥蛋白（RH2）) 在他们的视网膜中。光转导级联基因遵循类似的个体发育模式，在大多数物种中，锥体后跟杆特异性基因表达，除了珍珠目和剑齿虎（Aulopiformes），其中锥体级联在整个发育过程中仍然占主导地位。通过检查五种深海物种的全基因组（其中四种在本研究中测序：Idiacanthus fasciola、Chauliodus sloani ; Stomiiformes; Coccorella atlantica和Scopelarchus michaelsarsi ; Aulopiformes），我们发现深海鱼拥有一到两个副本视杆蛋白RH1视蛋白基因和多达 7 个视锥细胞RH2拷贝视蛋白基因在其基因组中，而其他视蛋白类别已大部分丢失。因此，我们的研究结果为有限的视蛋白基因库和保守的脊椎动物模式提供了分子证据，其中视锥光感受器首先发育，杆状光感受器仅在后期发育阶段添加。