Comparative Transcriptome analyses of the molecular mechanisms underlying skin color variations in ocellaris clownfish Amphiprion ocellaris (Cuvier, 1830)

In this study, we employed high-throughput transcriptomic sequencing technology to analyze the skin color variations among four different strains of clownfish ( Amphiprion ocellaris ). We compared the differentially expressed genes (DEGs) between the Captive Breeding of A. ocellaris (RS), Australian Geographic Variation of A. ocellaris (AS), Wild-Caught A. ocellaris (YS), and Carnelian A. ocellaris (MS). Furthermore, we conducted Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to explore the enriched pathways associated with pigment regulation genes. The results revealed that there were 270 common DEGs across the four different strains of A. ocellaris . In comparisons of AS, YS, and MS against RS, the numbers of DEGs that were upregulated and downregulated were 932, 1925, and 1929, respectively. The GO functional annotation analysis across the four comparisons indicated that the DEGs involved in cellular processes were the most numerous. Finally, the KEGG pathway enrichment analysis revealed significant enrichment (p<0.05) in 11, 10, and 6 unique pathways in RS compared to AS, YS, and MS, respectively. Key biological pathways involved in body color variation included DNA replication, drug metabolism—cytochrome P450 pathways, and pigment biosynthesis. The findings of this study provide new insights into the molecular basis of body color variations among different strains of A. ocellaris and offer theoretical foundations for breed improvement in aquaculture.