Complete genome assembly of hydrothermal vent mussel Bathymodiolus thermophilus thioautotrophic symbiont

Mytilid mussel <em>Bathymodiolus thermophilus</em> lives in the deep-sea hydrothermal vent regions through a symbiotic relationship with chemosynthetic Gammaproteobacteria species. The mussel depends on the nutrient provided by the symbiont residing inside specialized gill cells. The symbionts in the gill bacteriocytes oxidize the reduced sulfur amply available in the vent environment. Here we sequenced and assembled the complete gill symbiont genome of an individual mussel from the East Pacific Rise (EPR9N), using PacBio sequencing technology. The final symbiont assembly consists of a single contig size of 2.83 Mb, with a GC content of 38.6% and encodes for 2,133 protein-coding genes. CRISPR diversity analysis confirmed that we sequenced a single symbiont strain. Comparative analysis revealed 2,554 core gene clusters were shared with other <em>B. thermophilus</em> thiotrophic gill symbiont genomes whereas 125 were unique to this EPR9N strain. These unique gene clusters included genes such as Ni,Fe-hydrogenases I subunits, rubredoxins, and hydrogenase maturation factors but were mainly comprised of various repeats, transposases and uncharacterized proteins. Variation in genome size, gene content and genome re-arrangement across individual hosts suggests multiple symbiont strains can associate with <em>B. thermophilus</em>. This complete mussel symbiont genome will be invaluable for further comparative genomic analyses studying structural genome evolution, symbiont population diversity, and symbiont ecology.贻贝科的*Bathymodiolus thermophilus*（深海热液贻贝）通过与化能合成型γ-变形菌门（Gammaproteobacteria）物种建立共生关系，栖息于深海热液喷口区。该贻贝依赖栖息于其特化鳃细胞内的共生菌所提供的营养物质，而鳃部细菌细胞内的共生菌可氧化喷口区环境中大量存在的还原性硫化物。本研究采用PacBio测序技术，对东太平洋海隆（East Pacific Rise, EPR9N）处一枚个体贻贝的鳃部共生菌完整基因组进行了测序与组装。最终获得的共生菌组装结果包含一条长度为2.83 Mb的重叠群（contig），其GC含量为38.6%，共编码2133个蛋白质编码基因。成簇规律间隔短回文重复序列（CRISPR）多样性分析证实，本次测序仅获得了单一的共生菌菌株。比较基因组分析显示，该菌株与其他*B. thermophilus*硫营养型鳃部共生菌基因组共拥有2554个核心基因簇，另有125个基因簇为EPR9N菌株所特有。这些特有基因簇包含镍铁氢化酶I亚基、红氧还蛋白（rubredoxins）以及氢化酶成熟因子等编码基因，但主要由各类重复序列、转座酶以及功能未表征蛋白构成。不同宿主个体间的基因组大小、基因组成以及基因组重排情况存在差异，这表明*B. thermophilus*可与多种共生菌菌株建立共生关系。这一完整的贻贝共生菌基因组将为后续开展结构基因组进化、共生菌种群多样性以及共生菌生态学相关的比较基因组分析提供宝贵的研究资源。