Transcriptomic identification of skin-enriched genes reveals the molecular basis of skin functional specialization in the coral hind (Cephalopholis miniata)

Fish skin is a multifunctional tissue that serves as a primary interface between the organism and its aquatic environment, integrating physical barrier, innate immune defense, metabolic homeostasis, and pigmentation functions. However, the molecular basis underlying skin specialization in coral reef-associated serranid fishes remains poorly understood. Here, we performed comparative transcriptomic analysis of five tissues—skin, gill, liver, muscle, and intestine—from healthy wild-caught coral hind ( Cephalopholis miniata ) to characterize the tissue-specific molecular features of skin. Transcriptome profiling revealed clear tissue-dependent expression patterns, with skin forming a distinct transcriptional cluster from the other tissues. Comparative analysis identified 1,495 genes consistently up-regulated in skin relative to gill, liver, muscle, and intestine, representing a core skin-enriched gene set. Functional enrichment analyses demonstrated that these genes were predominantly associated with extracellular matrix organization, cell adhesion, epithelial structure and barrier formation, innate immune defense, glutathione metabolism, arachidonic acid metabolism, and pigmentation-related processes. Representative genes involved in extracellular matrix and epithelial integrity, including COL11A1, COL7A1, COL6A2, SPARC, LAMB4, ITGA6, and ITGB4, showed strong skin-biased expression, suggesting an enhanced structural barrier system. Concurrent enrichment of complement components, defensin-, lysozyme-, and chemokine-related genes indicated a constitutive innate immune surveillance program. Genes associated with glutathione metabolism, such as GPX7, GPX8, and GSS, together with arachidonic acid metabolism-related genes including ALOX5, ALOX5B, and PTGDSB, further suggested active redox and lipid-mediated homeostatic regulation. Notably, pigmentation-associated genes, including MITFA, TYRP1B, PMELA, melanoregulin, and Wnt-family genes, were also enriched in the skin transcriptome, indicating that pigment-cell-related processes are an intrinsic component of skin molecular specialization. Overall, our results demonstrate that C. miniata skin possesses a coordinated transcriptional program integrating epithelial barrier integrity, innate immunity, metabolic homeostasis, and pigmentation. The identified skin-enriched genes provide a candidate molecular framework for understanding the specialized ecological and physiological functions of serranid fish skin and provide valuable targets for future functional and spatial validation.