Wholegenome DNA methylation atlas of the scallop Patinopecten yessoensis

DNA methylation, a fundamental epigenetic mechanism in eukaryotes, yet remains inadequately studied in the second-largest animal phylum, Mollusca. This gap persists due to a lack of comprehensive cross-tissue methylome data, which has hindered a deeper understanding of its regulatory roles in various organs in molluscs. To address this, we utilized the Yesso scallop (Patinopecten yessoensis), which retains most of the ancestral bilaterian gene families as a model system. Employing whole-genome bisulfite sequencing (WGBS), we constructed a high-resolution DNA methylation atlas spanning nine organs, including shell, striated muscle, mantle, hepatopancreas, blood, kidney, smooth muscle, gill, and foot. This approach produced 4.9 billion high-quality clean reads with robust biological reproducibility. Clustering analysis indicated that muscle tissues and blood share notable epigenetic similarities. In contrast, the shell displayed distinct methylation landscapes, likely reflecting its highly specialized functions in hematopoiesis and stem cell maintenance. Our data offers new perspectives on the involvement of DNA methylation in organ specialization in molluscs.