Single-cell transcriptomics reveals the regulation of bco1 and bco2 genes in the carotenoid metabolism of koi carp.

The koi carp is a highly valued ornamental fish with a variety of skin color patterns that play an important role in survival and reproduction, but the molecular basis of these conspicuous colors remains obscure. Here, we generated a single-cell atlas of the red and white skin of Kohaku koi. We found that the skin tissue could be divided into 10 cell types, of which epithelial cells, endothelial cells, fibroblasts and xanthophores were present in higher proportions. Interestingly, pseudotime analysis revealed that pigment cells developed from white to red skin, and genes related to the uptake and degradation of carotenoids were significantly upregulated in red skin. Functional studies using TEM, HPLC, ISH, immunofluorescence, RNAi, cell culture, gene editing, RNA-seq and gene family analysis showed that k-bco2 could access more substrates than k-bco1, and that the two genes do not interact directly but may act synergistically via the calcium-ion signaling pathway. These insights enhance our understanding of pigment cell development and differentiation in fish, and the scRNA-seq transcriptome profiles offer valuable implications for future molecular breeding strategies.