Combined analysis of ATAC-Seq, RNA-Seq and GWAS reveals glycogen metabolism regulatory network in Jinjiang oyster Crassostrea ariakensis

Glycogen is the most effective energy reserve for metabolism in aquatic shellfish, and also contributes to the flavor and quality of oyster. Jinjiang oyster Crassostrea ariakensis is an economically and ecologically important species in China. In this study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed respectively to explore the gene expression and dynamic changes of chromatin accessibility among the oysters with different glycogen contents. A total of 9483 differentially expressed genes (DEGs) and 7215 significantly differential chromatin accessibility genes (DCAGs) were obtained, with the intersection of DEGs and DCAGs reaching 2600. Many of those genes were enriched in the pathways related to glycogen metabolism such as "Glycogen metabolic process" and "Starch and sucrose metabolism". In addition, a total of 526 SNP loci associated with glycogen content obtained by the genome wide association study (GWAS) corresponded to 241 genes, 63 of which were also DEGs and DCAGs as revealed above. This study will enrich basic research data and provide insights into the molecular mechanisms underlying the regulation of glycogen metabolism in oyster.