Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialised macrobenthos such as mussels. But lack of genome information hinders understanding of the adaptation of these animals to such inhospitable environment. Here we report the genomes of a deep-sea vent/seep mussel Bathymodiolus platifrons and a shallow-water mussel Modiolus philippinarum. Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilising protein structures and removing toxic substances from the cells, are greatly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The B. platifrons innate immune system is considerably more complex than that of other lophotrochozoan species including M. philippinarum, with significant expansion and high expression of gene families related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons found methanotrophy, assimilatory sulfate reduction, and ammonia metabolic pathways in the symbionts, providing energy and nutrients to allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.

热液喷口（Hydrothermal vents）与甲烷冷泉（methane seeps）是一类极端深海生态系统，其支撑着以贻贝为代表的特化大型底栖生物（macrobenthos）的高密度种群。但基因组信息的匮乏阻碍了学界对这类动物适应此类极端恶劣环境的机制的理解。本研究报道了深海热液/冷泉栖居的平端深海贻贝（Bathymodiolus platifrons）以及浅水型菲律宾偏顶蛤（Modiolus philippinarum）的基因组。系统发育分析（phylogenetic analysis）显示，这两类贻贝物种大约在1.104亿年前发生分化。诸多基因家族（gene families）——尤其是参与稳定蛋白质结构与清除细胞内有毒物质的基因家族——在平端深海贻贝中发生了显著扩增，这提示其对极端环境的适应性演化。平端深海贻贝的先天免疫系统（innate immune system）远比包括菲律宾偏顶蛤在内的其他冠轮动物（lophotrochozoan）更为复杂：其鳃组织中与免疫识别（immune recognition）、胞吞作用（endocytosis）以及半胱天冬酶介导的细胞凋亡（caspase-mediated apoptosis）相关的基因家族呈现显著扩增与高表达特征，这揭示了深海贻贝针对其化能自养内共生体（chemoautotrophic endosymbionts）的潜在遗传适应性机制。后续针对平端深海贻贝鳃组织的宏蛋白质组分析（metaproteomic analysis）发现，其共生体（symbionts）中存在甲烷氧化作用（methanotrophy）、同化硫酸盐还原（assimilatory sulfate reduction）与氨代谢通路（ammonia metabolic pathways），这些过程可为宿主提供能量与营养，支撑其种群繁盛。本研究针对极端环境软体动物（extremophile molluscs）的共生相关基因组特征展开解析，为深海管蠕虫（deep-sea tubeworms）、巨蛤（giant clams）等其他生物的共生机制研究提供了更广阔的认知视角。