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A variety of shell colors are one of the most fundamental characteristics of molluscs,which have importantly ecological and economic significance.The Pacific oyster Crassostrea gigas is distributed in many sea areas around the world and also an aquacultured mollusc with high nutritional value.In this study,the whole soft body and the mantle tissue of black-shelled Pacific oyster(BSO)and white-shelled Pacific oyster(WSO)with starkly different melanin contents were compared,and the differences in physiology and metabolism between BSO and WSO were analyzed.The results of physiological indicators suggested BSO show more melanin,more dry matter,more crude lipid content,and stronger ability to scavenge free radicals than WSO.The altered metabolites of glycerophospholipids,fatty acyls,and steroids revealed different regulatory mechanisms of lipids.The correlation analysis of metabolomics and previously published RNAseq data suggested that BSO and WSO mainly differed in the basal metabolic processes,such as lipid,amino acid and purine metabolisms.This study provides insights into the changes in the physiological indictors and the metabolites of oysters with varying melanin content.