Integrated Analysis of Skin Development and Pigmentation in Amphiprion frenatus: Insights from Histology, Transcriptomics, and Translatomics

Skin pigmentation in teleosts is a complex process governed by molecular and cellular mechanisms during development. In this study, we investigated the pigmentation process in the tomato clownfish (Amphiprion frenatus) using an integrated approach combining histological analysis, transcriptomics (RNA-Seq), and translatomics (Ribo-Seq). Histological examination revealed the stepwise differentiation of melanophores, xanthophores, and iridophores during post-embryonic development. Transcriptomic profiling between 0 and 14 days post-hatching (dph) identified 4,245 differentially expressed genes associated with metabolism, pigment biosynthesis, and extracellular matrix remodeling. The integration of transcriptomic and translatomic data revealed extensive post-transcriptional regulation, with many genes displaying discordant changes in mRNA and protein levels. Quantitative PCR analysis at 25 and 40 dph confirmed the dynamic upregulation of genes involved in cell proliferation (myc, pcna), pigment transport (myo5a, rab38), and pigment cell signaling (mchr1, ggt1). These findings demonstrate that pigmentation in A. frenatus is controlled through a multilayered regulatory network that involves both transcriptional and translational mechanisms. This study offers new insights into the molecular basis of chromatophore development and pigment pattern formation in coral reef fish species.