Butter clam genome assembly and analysis reveals the historical adaptation of shellfish genome to changes in the marine environment

Purple butter clam (Saxidomus purpuratus) is an economically important bivalve shellfish. This species belongs to the subclass Heterodonta that diverged in calcite seas with low magnesium concentrations. We sequenced and assembled its genome and performed an evolutionary comparative analysis. A total of 911 Mb assembly of S. purpuratus was anchored into 19 chromosomes and a total of 48,090 protein-coding genes were predicted. We identified its repeat-based expanded genes that are associated with the sodium/potassium-exchange ATPase complex. In addition, different types of ion transporters were enriched in the common ancestor of Heterodonta (calcium, sulfate, and lipid transporters) and the specific evolution of S. purpuratus (calcium and sodium transporters). These differences seem to be related to the divergence times of Heterodonta (calcitic sea) and Veneraidea (aragonitic sea). Furthermore, we analyzed the evolution of scavenger receptor (SR) proteins in S. purpuratus, which are involved in a wide range of immune responses, and compared them to the closely related Cyclina sinensis. We showed that a small number of SR proteins, exhibited collinearity between the two genomes, which is indicative of independent gene evolution. Our genomic study provides an evolutionary perspective on the genetic diversity of bivalves and their adaptation to historical changes in the marine environment.

Impacts of bioturbation by Venus clam Cyclina sinensis (Gmelin, 1791) on benthic metabolism and sediment nutrient dynamics in a shrimp-clam polyculture pond

Dynamics of benthic inorganic nutrients are key biogeochemical components of sediment metabolism and ecosystems. This study investigated the roles of the bivalve Cyclina sinensis (Gmelin, 1791) and its influence on benthic metabolism, nutrient fluxes and sediment oxygen consumption (SOC) in a shrimp-clam polyculture system in comparison with shrimp culture ponds without incorporating clams, in Ningbo Zhejiang China. The benthic inorganic nutrients fluxes (ammonium-NH4+, nitrate plus nitrite-NO3-+NO2- and phosphate-PO43-) and SOC were measured across the sediment-water interface with dark incubation experiments. The results showed that there were significantly higher nutrient fluxes from the sediment into the overlying water (p<0.05) in the treatment ponds in the order of NH4+ > PO43- > NO3- + NO2-. The SOC varied significantly (p<0.05) and was three-times higher than that of the control ponds. Water quality (dissolved oxygen, pH, chlorophyll-a and salinity) recorded showed slight variations over time but were not significantly different (p>0.05) between the control and treatment ponds. Sediment organic matter and chlorophyll-a concentration measured in the shrimp-clam ponds varied significantly (p<.05) as compared to control ponds. The results of this study suggest that the bioturbation activities by C. sinensis promoted the SOC, sediment organic matter degradation and mineralisation process that increased the exchange of nutrients and oxygen uptake between the sediment and the overlying water.