Integrated analysis of the mantle methylome and transcriptome in Cyclina sinensis provides new insights into the molecular mechanisms of shell color formation

Cyclina sinensis is an economically important bivalve in shallow-sea aquaculture, whose shell color is a key phenotypic trait with implications for ecological adaptation and commercial value. This study reports the first genome-wide DNA methylation profile of the mantle tissue from purple-shelled and white-shelled C. sinensis using Oxford Nanopore Technologies (ONT). We generated an average of 28.06 Gb of high-quality data per sample and identified 65,649 differentially methylated regions (DMRs), categorized as 36,130 6 mA, 24,689 CHH, 4998 CHG, and 1832 CpG sites. Functional analysis revealed significant enrichment of DMR-related genes in key pathways such as phosphatidylinositol signaling, calcium signaling, and ECM-receptor interactions. Integrated methylome and transcriptome analysis highlighted several critical genes, including elovl4 (lipid metabolism), calm (calcium signaling), and cyp1a1 (pigment metabolism), that potentially regulate carotenoid transport in purple-shelled individuals. Key regulators such as PTP10D, FBN1, and interferon-induced genes were also identified, along with transcription factors from the bHLH and bZIP families that were strongly correlated with shell color. These findings provide novel insights into the epigenetic mechanisms underlying shell color formation and establish a foundation for the molecular breeding of C. sinensis . • First nanopore-based mantle methylome of C. sinensis reveals shell color epigenetics. • 67,649 DMRs identified between shell color morphs. • DMR-genes enrich in PI/calcium signaling and ECM-receptor pathways. • Integrated omics reveals key regulators (PTP10D, FBN1, interferon-related genes).