Integrated analysis of the role of miRNA-mRNA in determining different body colors of leopard coral grouper (Plectropomus leopardus)

Abstract MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression at the post-transcriptional level and play important roles in many biological processes, including controlling body color differentiation in many different animals. However, the mechanism by which specific miRNAs regulate body color formation in leopard coral groupers has remained largely elusive. In the present study, we sequenced the miRNAs of red and black skin samples from leopard coral grouper (Plectropomus leopardus) with the Illumina HiSeq X_Ten platform to explore the function of miRNAs in the body color formation. A total of 15.21 M and 13.69 M high quality reads were obtained from the black and red skin samples, respectively. Within these sequences, 626 known and 354 novel miRNAs were identified. When comparing across the two groups, we found 60 differentially expressed miRNAs, with red-colored group having 44 up-regulated miRNAs including miR-215, miR-2188, miR-194, miR-122, novel-m0118, and 16 down-regulated miRNAs including miR-187, novel-m0189, novel-m0145, compared to black-colored group (p   1). Integrated analysis of differentially expressed miRNAs and mRNAs identified 846 miRNA-mRNA pairs with opposite expression patterns. Go terms and KEGG pathway enrichment analyses showed that these putative target mRNAs were enriched for functions involving in endocrine systems, immune response, and lipid metabolism. The present study shows the potential role of miRNAs in the body color formation of fish and provides a molecular foundation to explain the role of epigenetics in fish body color selections.