Dietary Supplementation of β-Carotene Reveals miRNAs Involved in the Regulation of Carotenoid Metabolism in Crassostrea gigas

Carotenoids play crucial physiological roles in animals. A comprehensive investigation into the mechanism of carotenoid metabolism in oysters will establish a theoretical foundation for further development of its carotenoid-rich traits. However, the information on the function of miRNA in β-carotene metabolism in oysters is limited. To elucidate the mechanisms underlying miRNA regulation of carotenoid metabolism in oysters, we compared the expressions of miRNA in digestive gland tissues of Pacific oyster (Crassostrea gigas) fed with a β-carotene supplemented diet and a normal diet, respectively. A total of 690 candidate miRNAs in the Pacific oyster digestive gland tissues were identified, including 590 known miRNAs and 111 unknown miRNAs. Three differentially expressed miRNAs were obtained in the carotenoid-fed and normal groups, associated to 137 differentially expressed target genes. Moreover, the GO enrichment analysis revealed that the differentially expressed target genes were mainly involved in transmembrane transport activity. KEGG enrichment showed that the differentially expressed target genes were involved in ABC transport. Analysis of the mRNA-miRNA network revealed that novel0025 played a central role in carotenoid metabolism, and it was negatively correlated with the expression of 46 mRNAs. In addition, down-regulated expression of novel0025 upregulated the expression of the lipoprotein gene LOC105342186, suggesting a potential regulatory role in carotenoid metabolism. Our results provide useful information for elucidating the miRNA regulation mechanism during carotenoids metabolism in the Pacific oyster.