Multi-omics approaches provide insights into adaptation to low salinity of intertidal clams

Climate change is reshaping the population distribution of intertidal organisms, with extreme weather inducing salinity fluctuations that challenge intertidal bivalves. In this study, we employed comparative genomics and transcriptomic analyses to investigate the molecular mechanisms underlying low-salinity adaptation in the razor clam (Sinonovacula constricta). We compiled and analyzed genomic data from 19 molluscan species, classified as either euryhaline or stenohaline based on their salinity tolerance. Phylogenetic analysis suggested that partial Venerida clams may have been evolved into adaptation to low salinity environments at 86.45 Mya (million year ago), or earlier. A total of 440 genes in S. constricta genome were detected to be under positive selection through within-species comparison. Furthermore, we identified sixty-nine lipid metabolism-associated orthologous groups (OGs), including four specially expanded gene families in five intertidal bivalves. Additionally, we constructed twenty-seven transcriptomic libraries from gill, mantle and digestive gland tissues of S. constricta, revealing the species employs complex molecular mechanisms in response to low-salinity stress. Twenty-eight positive selected genes exhibited significant differential expression in razor clam transcriptomic data. By integrating genomic and transcriptomic data, we identified candidate genes involved in CDP-choline, CDP-ethanolamine pathways that enhance phospholipid synthesis in S. constricta, potentially representing an adaptive mechanism to low-salinity environments. Notably, we found the lack of Cav2 member of caveolin family in euryhaline clams, which involved in Caveolae formation promoted by phospholipid. These findings enriched our understanding of the adaptive mechanisms and taxonomic characteristics of intertidal bivalves.