Multiomics provided insights into the molecular mechanisms underlying black-colored mantle in scallops

Abstract

Abstract Systematic development of genetic breeding should be based on a good understanding of good growth traits, e.g., color traits, which can greatly influence organismal function. Melanin greatly influences the physiological functions of organisms; however, such studies on scallops are scarce. In this study, we collected the black mantle tissues from Bohai Red scallops and sequenced the transcriptome and metabolome, with normal-colored (white) mantle tissues as control (three black and three normal). Our results revealed that the pigment component in the black mantle of scallops was indeed melanin. Based on the transcriptome data, 1314 differentially expressed genes were obtained and subjected to the Gene Ontology (GO) enrichment analysis. The upregulated genes in the black mantle were mainly enriched in transition metal ion binding, hydrolytic enzyme activity, and copper ion binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the up- and downregulated genes were enriched in different pathways, suggesting that the pathways for the formation of the black mantle were unique. Several candidate genes associated with black mantle formation in scallops were identified. Among them, the downregulation of MAO and GST genes and upregulation of CYP3A and PKA genes may have a positive effect on the formation of black mantle in scallops. The differentially expressed metabolites were mainly enriched in metabolism-related biological pathways. This suggested that the formation of black mantle in scallops may affect physiological functions related to metabolism in scallops. Therefore, this study revealed several candidate genes related to the formation of black mantle in scallops via multiomics and provided a theoretical basis for breeding scallops with black mantle with high economic value.