Weighted gene co-expression network analysis reveals the mechanisms of evolutionary adaptation and selection behind blind-side hypermelanosis in Chinese tongue sole (Cynoglossus semilaevis)

Chinese tongue sole is an important flatfish widely cultured in coastal areas in China. Blind-side hypermelanosis has been emerged as a major concern in the last decade in flatfish. However, the causative factors and specific mechanisms have yet not been well addressed. To unscramble the underlying genetic basis behind this economic trait from the perspective of key hub genes and regulatory modules, in the present study, RNA sequencing based weighted gene co-expression network analysis was performed in tongue sole. Overall, three modules (darkturquoise, darkgreen and midnightblue) were identified as key modules significantly associated with pigmentation. There were 49, 13 and 49 hub genes in darkturquoise, darkgreen and midnightblue modules respectively. Hub genes in darkturquoise module were mainly functioned in tyrosine metabolism and melanogenesis related processes or pathways. Interestingly, some hub genes in darkgreen module (e.g., spp1, tgfb2, and col5a2) were identified as selection signatures associated with growth (body size, carcass, and muscle development); while some hub genes in midnightblue module were selection signatures associated with reproduction (e.g., zp3, tspan1, and tspan13) or immune (b3galnt2). Combined the enrichment analysis results that the genes in darkgreen module were mainly functioned in bone formation, skeletal development and cardiomyopathy related processes and pathways, which well addressed the adaptation of benthic colonization of flatfish. Finally, these new findings further increased the credibility of our hypothesis, that the blind-side hypermelanosis is drove by environmental adaption and selection. The results provided deeper insights into the genetic basis of blind-side hypermelanosis in flatfish. •Key hub genes and modules associated with hypermelanosis were identified via WGCNA.•Some key hub genes are identified as selection signatures of economic traits.•Blind-side hypermelanosis is drove by environmental adaptation and selection.