The sea cucumber Holothuria leucospilota is an economically and ecologically important tropical species. Following development into juveniles, H. leucospilota undergoes a color change from white to black, involving a pigmentation process for over a period of several months. In this study, a combination of liquid chromatography-tandem mass spectrometry (LC–MS/MS) and Next-Generation sequencing (NGS) were employed to investigate the changes in metabolomic and transcriptomic profiles during pigmentation in H. leucospilota juveniles. The metabolomic analysis identified a total of 341 metabolites, of which 52 were found to be differentially regulated (P < 0.05 and VIP > 1), with 27 being upregulated in white individuals and 25 in black individuals. Additionally, 632 differentially expressed genes (DEGs) were identified, with 380 genes upregulated in white samples and 252 genes upregulated in black samples. Interestingly, the melanin content and tyrosinase transcript levels did not display significant differences between the two groups. Metabolomic data suggested the involvement of the linoleic acid metabolic pathway in pigmentation. Transcriptomic analysis, coupled with realtime PCR validation, revealed a decrease in the transcript levels of digestive enzymes like α-amylase, maltase-glucoamylase, and trehalase after the juveniles changed to black. Furthermore, the mRNA expressions of major yolk proteins showed a decline, indicating a shift in the accumulation of protein nutrient sources. Overall, our findings suggest that during the pigmentation process in H. leucospilota, no significant changes were observed in the classical melanin pathway, while notable alterations were observed in their nutritional status. This study provides valuable insights into the regulatory mechanisms of pigmentation in marine organisms.

海参Holothuria leucospilota是一种具有重要经济和生态意义的热带物种。发育成幼体后，白斑海螺会经历从白色到黑色的颜色变化，涉及长达数月的色素沉着过程。在本研究中，采用液相色谱-串联质谱（LC-MS/MS）和下一代测序（NGS）相结合的方法来研究H. leucospilota幼鱼色素沉着过程中代谢组学和转录组学谱的变化。代谢组学分析总共鉴定出 341 种代谢物，其中 52 种被发现存在差异调节（P  < 0.05 且 VIP > 1），其中 27 种在白人个体中上调，25 种在黑人个体中上调。此外，还鉴定出 632 个差异表达基因 (DEG)，其中 380 个基因在白人样本中上调，252 个基因在黑人样本中上调。有趣的是，两组之间的黑色素含量和酪氨酸酶转录水平没有显示出显着差异。代谢组学数据表明亚油酸代谢途径参与色素沉着。转录组分析结合实时 PCR 验证显示，幼鱼变成黑色后，α-淀粉酶、麦芽糖酶-葡萄糖淀粉酶和海藻糖酶等消化酶的转录水平下降。此外，主要卵黄蛋白的mRNA表达量呈下降趋势，表明蛋白质营养来源的积累发生了变化。总体而言，我们的研究结果表明，在H. leucospilota的色素沉着过程中，经典黑色素途径没有观察到显着变化，但其营养状况却发生了显着变化。这项研究为海洋生物色素沉着的调节机制提供了宝贵的见解。