Glass scallop genome reveals key adaptations to deep-sea environments and ectosymbiosis

Chemosynthetic symbioses enable many deep-sea animals to flourish, yet the genomic basis of ectosymbiosis in deep-sea bivalves is poorly understood. We present a chromosome-level genome for the glass scallop Catillopecten margaritatus, the only scallop known to host sulphur-oxidising bacteria on its gills. The genome comprises a conserved set of 19 chromosomes shared with common scallops, and evolutionary analyses place the lineage split in the Early Devonian, predating the establishment of ectosymbiosis. Integrating genome, gene-expression, and shell chemistry data, we identify adaptations to deep-sea life and symbiosis: loss of vision, enhanced mantle sensing, reduced shell calcification, immune mechanisms that recognise and accommodate symbionts, robust sulphide detoxification, and host provisioning of metabolites to the bacteria. The species also retains predatory feeding, indicating mixotrophy. These results clarify how this species colonised chemosynthetic habitats, broaden the spectrum of symbiotic strategies in bivalves, and provide a genomic framework for testing transitions from asymbiosis to symbiosis. Endocsymbiosis is known to fuel deep-sea life, while ectosymbiosis remains poorly understood. Analysing the genome of a cold-seep scallop, this study uncovers key adaptations to the deep sea and metabolic complementarity with chemosynthetic bacteria on its gill surface.