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.