Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika

Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins – but not the rhodopsin – rank among the most differentially expressed genes in the retina, together with other vision-, circadian-rhythm-, and haemoglobin-related genes. We propose two new visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes., In this study, we sequenced 753 new retinal transcriptomes of 112 cichlid species from African Lake Tanganyika to (i) identify adaptive changes in the expression of rod and cone visual opsin genes, (ii) define and reconstruct the evolution of visual palettes on the basis of cone opsin expression levels, and (iii) examine rod and cone opsin expression levels in relation to macro-habitat, diet, and relative eye size. Sampling of fish eyes was performed between 2014 and 2020 at 44 locations at Lake Tanganyika covering the entire north-south axis of this approximately 670 km long lake. For each specimen, the retina of a single eye was dissected, homogenised (FastPrep-24; MP Biomedicals), and the total RNA was extracted using the Direct-zol RNA kit (Zymo) according to the manufacturer’s protocol. Individual libraries were constructed using the Illumina TruSeq stranded protocol including RiboZero Gold rRNA depletion (Illumina) and sequenced on an Illumina NovaSeq 6000 in PE 100-bp mode. Libr..., A GitHub reposit is available for further information: https://github.com/Ninet93/RNASeq_Ricci_et_al在众多动物物种中，使视觉感官系统适配环境光照对于生存至关重要。这一过程通常通过视觉视蛋白（visual opsin）基因的复制、功能分化以及/或者差异表达来实现。 本研究针对来自坦噶尼喀湖（Lake Tanganyika）的112种慈鲷鱼类（cichlid fishes）的753份全新视网膜转录组（retinal transcriptome）进行分析，旨在解析这一全球最大的脊椎动物适应辐射（adaptive radiation）类群之一，在宏观进化与生态系统层面上的基因表达适应性变化。 研究发现，在该适应辐射类群中，全部7种视锥视蛋白（cone opsin）——而非视紫红质（rhodopsin）——与其他视觉相关、昼夜节律（circadian rhythm）相关以及血红蛋白（haemoglobin）相关基因一同位列视网膜中差异表达最为显著的基因之列。 我们分别提出了适配极浅水环境与深水环境物种的两种全新视觉调色板，并证实：沿宏观生境与食性这两大生态轴发生的视觉系统适应性变化，主要通过部分视锥视蛋白基因的表达变异实现。 本研究对来自非洲坦噶尼喀湖的112种慈鲷的753份全新视网膜转录组进行测序，旨在达成三个研究目标：（1）解析视杆视蛋白（rod opsin）与视锥视蛋白基因的表达适应性变化；（2）基于视锥视蛋白的表达水平，定义并重构视觉调色板的演化历程；（3）探究视杆与视锥视蛋白的表达水平与宏观生境、食性以及相对眼大小之间的关联。 本研究的鱼类眼组织采样工作于2014至2020年间在坦噶尼喀湖的44个点位开展，覆盖了这座全长约670公里的湖泊的完整南北轴线。对于每一份实验样本，我们均解剖单眼的视网膜组织，使用FastPrep-24匀浆仪（MP Biomedicals品牌）进行匀浆处理，并按照制造商的操作手册，使用Direct-zol RNA提取试剂盒（Zymo品牌）提取总RNA。随后采用Illumina TruSeq链特异性建库方案（包含RiboZero Gold核糖体RNA去除步骤，Illumina品牌）构建单个文库，并在Illumina NovaSeq 6000平台上以双端100bp模式进行测序。如需获取更多信息，可访问本研究的GitHub代码仓库：https://github.com/Ninet93/RNASeq_Ricci_et_al