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）是支撑贻贝等特化大型底栖生物（macrobenthos）高密度种群的极端深海生态系统。但基因组信息的匮乏，阻碍了学界对这些动物适应此类极端不适生环境的机制解析。本研究报道了深海热液/冷泉贻贝平端肌蛤（Bathymodiolus platifrons）与浅海贻贝菲律宾偏顶蛤（Modiolus philippinarum）的全基因组序列。系统发育分析显示，这两种贻贝约在1.104亿年前发生分化。平端肌蛤体内存在大量扩增的基因家族，尤以稳定蛋白质结构、清除细胞内有毒物质相关的基因家族扩增最为显著，这暗示其对极端环境的适应性进化。平端肌蛤的先天免疫系统相较于包括菲律宾偏顶蛤在内的其他冠轮动物（lophotrochozoan）类群更为复杂：其鳃组织中，与免疫识别、胞吞作用（endocytosis）及半胱天冬酶介导的细胞凋亡（caspase-mediated apoptosis）相关的基因家族发生了显著扩增且呈高表达状态，这揭示了深海贻贝适应其化能自养内共生体（chemoautotrophic endosymbionts）的潜在遗传机制。后续对平端肌蛤鳃组织的宏蛋白质组（metaproteomic）分析发现，其共生菌具备甲烷营养代谢、同化硫酸盐还原与氨代谢通路，可为宿主提供能量与营养以支持其繁盛生长。本研究通过解析极端环境软体动物的共生相关基因组特征，为深海管蠕虫、巨蛤等其他生物的共生机制研究提供了更广泛的理论参考。