Exploring the regulatory role of long non-coding RNAs in pigmentation in juvenile Plectropomus leopardus

Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides, playing crucial roles in various biological processes, including the regulation of body color in animals. The Leopard coral grouper (Plectropomus leopardus) exhibits a wide range of body colors and is particularly valued in the market for its red skin color. Nevertheless, studies on the role of lncRNA in juvenile body color formation in P. leopardus are limited. In this study, we selected juvenile P. leopardus sample with transparent skin at 26 days post hatching (dph) and red skin at 30 dph for lncRNA sequencing. We constructed lncRNA expression profiles in skin tissues to explore the molecular mechanisms underlying red body color formation. Differentially expressed lncRNAs (DELs) showed that 104 DELs were up-regulated and 187 DELs were down-regulated in red skin juvenile P. leopardus (PR) compared to transparent skin juvenile P. leopardus (PT). By reporting body colour genes in the existing literature, and then constructing lncRNA-mRNA network, as well as functional enrichment of lncRNA-mRNA target genes, DELs were found to be mainly involved in carotenoid metabolism and red pigmentation (such as MSTRG.9028.1, MSTRG.21543.1, etc.), melanin synthesis and pigmentation regulation (such as MSTRG.22153.1, MSTRG.7025.5, etc.). In addition, 'retinol metabolism, tyrosine metabolism, cholesterol metabolism, thyroid hormone signaling pathway, Wnt signaling pathway, and melanogenesis' were also involved in body colour regulation. These results suggest that DELs may contribute to body colour regulation. This study reveals the potential role of lncRNAs in the formation of body colour in juvenile P. leopardus, and lays the foundation for future studies on the molecular mechanism of body colour diversity in this species.