Golden coloration in mandarin fish (Siniperca chuatsi) is associated with reduced melanization and altered skin pigment composition

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Abstract
Golden coloration can arise from changes in pigment production, pigment cell composition, or the function of pigment-containing organelles. Here, we characterized a golden variant (GV) of mandarin fish (Siniperca chuatsi) using morphological examination, skin pigment quantification, RNA sequencing, and untargeted metabolomics. Compared with wild-type (WT) fish, GV fish exhibited reduced visible melanization, lower melanin and pteridine contents, and higher β-carotene content. Transcriptomic analysis identified 1,163 differentially expressed genes, including 677 upregulated and 486 downregulated in GV relative to WT. Despite reduced melanin deposition, several genes associated with melanogenesis and melanosome biology were upregulated. Pathway enrichment analysis of upregulated genes and gene set enrichment analysis further supported changes in pigmentation-related transcriptional programs. Untargeted metabolomics yielded 2,995 putative metabolite annotations and identified 509 candidate differential features. However, no feature was significant at q < 0.05 after Benjamini-Hochberg correction across all tested annotations. A feature putatively annotated as L-tyrosine showed higher signal intensity in GV and mapped to pathways also represented in the transcriptomic dataset. Together, these findings show that reduced melanization and altered pigment composition in GV coexist with increased expression of several pigmentation-related genes. The candidate metabolic features require further validation, and the genetic basis and cellular processes underlying reduced melanin deposition remain unresolved.

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