Multi-omics analysis of sea urchin ( Strongylocentrotus intermedius) adaptation to salt stress reveals epigenetic regulatory mechanisms

Increased precipitation and surface runoff due to global warming has reduced surface seawater and nearshore water salinity, affecting marine organism survival. Nevertheless, the epigenetic mechanisms underlying the adaptation of sea urchins (Strongylocentrotus intermedius) to low-salinity stress remains unknown. This study utilized response surface methodology to formulate growth models for S. intermedius at different salinity levels and shell diameters. Whole genome bisulphite sequencing, RNA-sequencing, and metabolome analysis were performed on low-salinity stressed sea urchins, and a total of 3006 differential methylated regions, 945 differential methylated genes, 886 differentially expressed genes, and 271 differential metabolites were identified. Multi-omics analysis revealed significant alterations in the gene expression and DNA methylation of key genes (e. g., SPHK2, Arpc1a, and SLC23A1) in S. intermedius under low-salinity stress conditions. These changes subsequently influenced the metabolism of substances, including sphingosine-1-phosphate, ethanolamine phosphate, vitamin C, taurine, and choline. These alterations impacted functions related to immunity, osmoregulation, and energy metabolism in the organism. This study was to comprehensively elucidate the epigenetic mechanisms of S. intermedius under low-salinity stress from the perspective of DNA-RNA-metabolites, providing new insights into salinity adaptation of marine invertebrates.