Integrated Transcriptomic Analysis of Skin Pigmentation Development in Amphiprion frenatus

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 and transcriptomics (RNA-Seq and Ribo-Seq). Histological examination revealed the stepwise differentiation of chromatophores during post-embryonic development. Transcriptomic profiling at 14 days post-hatching (dph) identified extensive changes in transcript abundance, with 2063 of 2667 differentially expressed unigenes (DEUs) upregulated relative to hatching. These genes predominantly governed innate defense, digestion, and early pigmentary development, driven by the enrichment of Gene Ontology (GO) terms including inflammatory response, digestion, and developmental pigmentation. Integration of transcriptomic and Ribo-Seq datasets identified widespread discordance between transcript abundance and ribosome-protected fragment (RPF) abundance. These discordant expression patterns suggest candidate post-transcriptional regulatory events during skin pigmentation development. Quantitative PCR analysis at 23 and 45 dph confirmed the dynamic upregulation of genes involved in cell proliferation (myc, pcna), pigment transport (myo5a, rab38), and pigment cell signaling (mchr1). These findings suggest that skin pigmentation is associated with the selected transcript-abundance differences in A. frenatus. This study offers new insights into the molecular basis of chromatophore development and pigment pattern formation in coral reef fish species.