Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
Genome Biol Evol. 2022 Aug 3;14(8). doi: 10.1093/gbe/evac109.
Harsh environments provide opportunities to study how different species adapt, at the molecular level, to similar environmental stressors. High hydrostatic pressure, low temperature, and absence of sunlight in the deep-sea environment are challenging conditions for gene expression, cell morphology and vision. Adaptation of fish to this environment appears independently in at least 22 orders of fish, but it remains uncertain whether these adaptations represent convergent evolution. In this study, we performed comparative genomic analysis of 80 fish species to determine genetic evidences for adaptations to the deep-sea environment. The 80 fishes were divided into six groups according to their order. Positive selection and convergent evolutionary analysis were performed and functional enrichment analysis of candidate genes was performed. Positively selected genes (pik3ca, pik3cg, vcl and sphk2) were identified to be associated with the cytoskeletal response to mechanical forces and gene expression. Consistent signs of molecular convergence genes (grk1, ednrb, and nox1) in dark vision, skin color, and bone rarefaction were revealed. Functional assays of Grk1 showed that the convergent sites improved dark vision in deep-sea fish. By identifying candidate genes and functional profiles potentially involved in cold, dark, and high-pressure responses, the results of this study further enrich the understanding of fish adaptations to deep-sea environments.
恶劣环境为研究不同物种如何在分子水平上适应相似的环境胁迫提供了机会。深海环境中的高静水压力、低温和缺乏阳光是对基因表达、细胞形态和视觉的挑战条件。鱼类对这种环境的适应似乎在至少 22 个鱼类目中独立出现，但这些适应是否代表趋同进化仍然不确定。在这项研究中，我们对 80 种鱼类进行了比较基因组分析，以确定适应深海环境的遗传证据。这 80 种鱼类根据其目分为六组。进行了正选择和趋同进化分析，并对候选基因进行了功能富集分析。鉴定出与细胞骨架对机械力和基因表达的反应相关的正选择基因（pik3ca、pik3cg、vcl 和 sphk2）。揭示了暗视力、皮肤颜色和骨骼稀疏中一致的分子趋同基因（grk1、ednrb 和 nox1）的迹象。Grk1 的功能测定表明，趋同位点改善了深海鱼类的暗视力。通过鉴定可能参与冷、暗、高压反应的候选基因和功能谱，本研究的结果进一步丰富了对鱼类适应深海环境的理解。
