Genome-wide DNA methylation response of Paralichthys olivaceus to Ulva prolifera decomposition effluent stress

Ulva prolifera decomposition in the Yellow Sea poses a significant ecological threat, leading to seawater acidification, nutrient fluctuations, and altered dissolved oxygen levels. Previous studies have primarily focused on patterns of U. prolifera decay and its effects on biogenic elements, whereas research on its impacts on fish germplasm resources, particularly at the epigenetic level, remains limited. This study employed whole-genome bisulfite sequencing (WGBS) alongside published transcriptomic data to investigate the dynamic DNA methylation in the liver of Paralichthys olivaceus exposed to decomposing U. prolifera effluent (0.28 g/L) for 14 days. Our results revealed that the overall methylation level decreased after exposure to U. prolifera decomposition effluent, possibly due to the up-regulated expression of the demethylation gene tet3. A total of 7,519 differentially methylated regions (DMRs) were identified, including 4,290 hypermethylated and 3,229 hypomethylated regions, with chromosome 2 containing the highest number of DMRs. Functional enrichment analysis of differentially methylated promoters (DMPs) identified key pathways, including the MAPK signaling pathway, p53 signaling pathway, alpha-linolenic metabolism and Th17 cell differentiation. We speculate that P. olivaceus enhances lipid metabolism to provide additional energy and support cell proliferation as adaptive mechanisms. Furthermore, two candidate genes (mapk12a and irf10) were selected for further validation using bisulfite sequencing PCR (BSP) and quantitative real-time PCR (qRT-PCR). Overall, these findings provide novel insights into the epigenetic responses of P. olivaceus to stress induced by algal decomposition, offering a molecular foundation for assessing the ecological toxicity of green tides.