Transcriptome analysis and candidate gene identification reveals insights into the molecular mechanisms of hypermelanosis in Chinese tongue sole (Cynoglossus semilaevis)

Abstract

Blind-side hypermelanosis has emerged as a major concern in flatfish aquaculture worldwide, including tongue sole (Cynoglossus semilaevis) in China. The causative gene and the molecular basis are still unclear. In this study, comparative transcriptome analyses were performed using different skin tissues of tongue sole: ocular-side normal (pigmented) skin, blind-side normal (non-pigmented) skin and blind-side hypermelanotic (pigmented) skin. Finally, 60 key hypermelanosis-related genes were mined, providing potential candidate gene resources involved in blind-side hypermelanosis. These genes were selected based on the log2(FoldChange) and false discovery rate (FDR) values (with corresponding P-Values < 0.05), and they were verified in other species to assess if they were directly or indirectly related to melanogenesis. The protein-protein interaction network of these 60 genes and the relationship between tyr and other key hypermelanosis-related genes were illustrated. The qRT-PCR validation of 16 differentially expressed genes (DEGs) showed that the data of qRT-PCR were consistent with those of RNA-seq. Further analyses revealed that the selected DEGs were significantly overrepresented in several pigment metabolic processes and in the melanogenesis pathway. Our results may imply that blind-side hypermelanosis is a pattern of environmental regulation of gene expression and adaptation in flatfish. Membrane transport proteins (such as OCA2 and SLC45A2) may serve as a “switch” for melanogenesis in tongue sole. Overall, this study provided novel insights into the molecular mechanism of hypermelanosis in flatfish species and will facilitate future selective breeding of tongue sole for this market-favoured trait in aquaculture.