Teleost fishes are notable for generating remarkably diverse pigment phenotypes, which constitute key substrates for natural and sexual selection. However,  hereditary color defects, pigmentation trait segregation in hybrids, or melanotic hyperpigmentation can severely undermine the economic returns of aquaculture production. Elucidating the pigmentation mechanisms in fish could provide theoretical guidance and technical support for scientific aquaculture in multiple aspects. The Danioninae subfamily encompasses up to four hundred distinct species that have evolved to exhibit a dazzling variety of pigment patterns, including horizontal stripes, vertical bars, spots or lack a clear pattern. The diverse pigmentation patterns of closely related species within Danio offer an excellent model to unravel the genetic mechanisms underlying pigment pattern evolution. We assembled genomes of 14 Danio and Danionella species. The two sister species D. rerio and D. aesculapii exhibit divergent patterns of horizontal stripes and vertical bars that are partly attributable to the divergence of the potassium channel gene kcnj13. We demonstrate that kcnj13 is required solely in melanophores for interactions with xanthophores and iridophores. Molecular analyses identified positive selection and structural variations in pigmentation genes igsf11 and gja5b, which were functionally diverged between spotted and striped species, proved by the interspecific complementation tests. Strikingly, convergent evolution occurred in the C-terminal domain of gja5b in both spotted species, suggesting recurrent causative changes. Our phylogenomic and functional analyses integrate to elucidate complex genomic changes driving phenotypic diversification in Danio. Overall, deciphering the precise molecular events dictating pigmentation will substantially assist quality enhancement and trait optimization in aquaculture regarding coloration.

Keywords. Pigmentation; Danio genus; Genome assembly; Phylogenetics