Integrative transcriptomic and metabolomic analysis of body color formation in transparent goldfish (Carassius auratus).

The mechanism underlying the transparent body coloration in goldfish (Carassius auratus) remains unclear. This study employed untargeted metabolomics and transcriptomics analyses of scales, skin, and muscle tissues from transparent goldfish (T) and common goldfish (L), revealing that the transparent phenotype stems from systemic disruption of the purine metabolism network. Metabolomic analysis revealed significant downregulation of guanine and its precursor guanosine across all tissues. Correspondingly, transcriptomic analysis further demonstrated tissue-specific dysregulation of key genes involved in purine synthesis and conversion (mpv17 and pnp4a), collectively preventing iridophore cells from synthesizing sufficient reflector granules and resulting in the loss of structural coloration. Beyond iridophores, this purine metabolic abnormality triggered cascading dysfunctions across the pigment cell network. In melanocytes, the differentiation driver mitfb was upregulated while the synthesis executor tyrp1 was silenced, exemplifying a pattern of enhanced signaling but blocked execution. Compensatory upregulation of the carotenoid transport gene scarb1 also failed to complete pigment deposition. This study, for the first time through integrated metabolomic and transcriptomic analyses, systematically reveals the cascade effects triggered by purine metabolic dysregulation in transparent goldfish and elucidates the molecular mechanism by which purine metabolism disruption impairs iridophore function and further leads to abnormalities in the entire pigment cell system. It offers a new theoretical framework for understanding the evolution and artificial regulation of fish coloration.