Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Department of Biology, Hong Kong Baptist University, Hong Kong, China.
BMC Genomics. 2018 May 24;19(1):394. doi: 10.1186/s12864-018-4720-z.
High hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motility, can be disrupted by high hydrostatic pressure. High hydrostatic pressure can also damage DNA. Nucleic acids exposed to low temperatures can form secondary structures that hinder genetic information processing. To study how deep-sea creatures adapt to such a hostile environment, one of the most straightforward ways is to sequence and compare their genes with those of their shallow-water relatives.
We captured an individual of the fish species Aldrovandia affinis, which is a typical deep-sea inhabitant, from the Okinawa Trough at a depth of 1550 m using a remotely operated vehicle (ROV). We sequenced its transcriptome and analyzed its molecular adaptation. We obtained 27,633 protein coding sequences using an Illumina platform and compared them with those of several shallow-water fish species. Analysis of 4918 single-copy orthologs identified 138 positively selected genes in A. affinis, including genes involved in microtubule regulation. Particularly, functional domains related to cold shock as well as DNA repair are exposed to positive selection pressure in both deep-sea fish and hadal amphipod.
Overall, we have identified a set of positively selected genes related to cytoskeleton structures, DNA repair and genetic information processing, which shed light on molecular adaptation to the deep sea. These results suggest that amino acid substitutions of these positively selected genes may contribute crucially to the adaptation of deep-sea animals. Additionally, we provide a high-quality transcriptome of a deep-sea fish for future deep-sea studies.
高压和低温使深海成为生命形式的恶劣环境。肌动蛋白组织和微管组装对于细胞内运输和细胞运动至关重要，但它们会被高压破坏。高压还会破坏 DNA。暴露在低温下的核酸可以形成阻碍遗传信息处理的二级结构。为了研究深海生物如何适应这种恶劣的环境，最直接的方法之一是对它们的基因进行测序和与浅海近亲的基因进行比较。
我们使用远程操作车辆 (ROV) 在冲绳海槽水深 1550 米处捕获了一种典型深海生物—— Aldrovandia affinis 的个体。我们对其转录组进行了测序并分析了其分子适应机制。我们使用 Illumina 平台获得了 27633 个蛋白质编码序列，并将其与几种浅海鱼类进行了比较。对 4918 个单拷贝直系同源基因的分析鉴定出 Aldrovandia affinis 中 138 个正选择基因，包括参与微管调节的基因。特别是，深海鱼类和深海端足类动物中与冷休克和 DNA 修复相关的功能域都受到正选择压力的影响。
总体而言，我们鉴定出了一组与细胞骨架结构、DNA 修复和遗传信息处理相关的正选择基因，这些基因揭示了分子适应深海的机制。这些结果表明，这些正选择基因的氨基酸替换可能对深海动物的适应至关重要。此外，我们为深海鱼类的未来深海研究提供了高质量的转录组。
