Comparative transcriptomics identifies key genes and pathways underlying the early skin coloration in leopard coral...

The leopard coral grouper (Plectropomus leopardus) is a valuable marine economic fish, whose body color (especially red coloration) is a key trait determining its economic value. During early development, the body color of this fish transitions from transparent to red, providing an ideal model for elucidating the molecular mechanisms of body color formation. This study selected two critical time points, 26 dph(transparent)and 30 dph(red) post-hatching, to collect transparent skin (TC) and red skin (RC) tissues for comparative transcriptome analysis. Using the thresholds of |Fold Change| ≥ 2 and FDR < 0.05, a total of 1747 differentially expressed genes (DEGs) were identified, including 1213 up-regulated and 534 down-regulated genes, indicating that the formation of red body color involves the coordinated action of multiple genes. Further analysis revealed differential expression of several genes related to body color formation, including carotenoid metabolism-related genes (e.g., scarb1, ttc39b, bco2, fabp2, fabp3, apod, stard9) and melanin synthesis-related genes (e.g., tyr, tyrp1, dct, foxd3a). KEGG enrichment analysis showed significant enrichment of pathways related to lipid metabolism (e.g., steroid biosynthesis, cholesterol metabolism, arachidonic acid metabolism), melanin synthesis pathways (e.g., the Wnt signaling pathway and melanogenesis), and other potentially related pathways (e.g., retinol metabolism, insulin signaling pathway, purine metabolism), suggesting these pathways may collectively participate in the regulation of the body color transition. Furthermore, validation of 11 genes by qPCR confirmed the reliability of the RNA-seq data. This study highlights key molecular features during the early transition from transparent to red body color in the leopard coral grouper, providing new experimental evidence and a theoretical basis for a deeper understanding of its body color formation mechanisms.