Comparative miRNA-seq analysis revealed molecular mechanisms of red color formation in the early developmental stages of Plectropomus leopardus

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in several biological processes, including the regulation of body color. Leopard coral grouper (Plectropomus leopardus) is a valuable marine aquaculture fish; however, at present, there are no published reports on its early body color development. The skin color of P. leopardus undergoes a transition from transparent to red from 26 days post-hatching (dph) to 30 dph. In this study, we performed miRNA sequencing on 26 dph (Transparent, PT) and 30 dph (Red, PR) skin samples of P. leopardus to explore the molecular mechanism underlying red color formation. A total of 44.31 M and 37.55 M clean tags were obtained from PT and PR group, respectively. Among these tags, 981 miRNAs were identified, including 493 known and 488 novel miRNAs. A total of 106 differentially expressed miRNAs (DEMs) were identified in PT vs. PR, with 43 up-regulated and 63 down-regulated miRNAs in the PR group, compared to the PT group (|fold change| > 2 and p-value < 0.05). A miRNA-mRNA network based on 18 candidate miRNAs and 53 target genes related to pigmentation, and KEGG enrichment analysis of the target genes of all DEMs, revealed that miRNAs involved in the formation of red skin color were mainly related to: 1) the inhibition of melanin synthesis (miR-141-z, miR-206-z, miR-206-y, miR-27-z, miR-137-y, miR-204-x, miR-204-y, miR-211-x, miR-211-z); 2) chromatophore development (miR-206-z, miR-206-y, miR-499-y, miR-1-z, miR-2188-x, miR-423-x); and 3) carotenoid metabolism (miR-204-x, miR-204-y, miR-499-y). This study demonstrates the potential role of miRNAs in red color formation and lays the foundation for the molecular mechanism of body color polymorphism in P. leopardus.