Both sexual reproduction and unisexual reproduction are adaptive strategies for species survival and evolution. Unisexual animals have originated largely by hybridization, which tends to elevate their heterozygosity. However, the extent of genetic diversity resulting from hybridization and the genomic differences that determine the type of reproduction are poorly understood. In Carassius auratus, sexual diploids and unisexual triploids coexist. These two forms are similar morphologically but differ markedly in their modes of reproduction. Investigation of their genomic differences will be useful to study genome diversity and the development of reproductive mode. We generated transcriptomes for the unisexual and sexual populations. Genes were identified using homology searches and an ab initio method. Estimation of the synonymous substitution rate in the orthologous pairs indicated that the hybridization of gibel carp occurred 2.2 million years ago. Microsatellite genotyping in each individual from the gibel carp population indicated that most gibel carp genes were not tri-allelic. Molecular function and pathway comparisons suggested few gene expansions between them, except for the progesterone-mediated oocyte maturation pathway, which is enriched in gibel carp. Differential expression analysis identified highly expressed genes in gibel carp. The transcriptomes provide information on genetic diversity and genomic differences, which should assist future studies in functional genomics.

The blood parrot cichlid (Cichlasoma citrinellum × C. synspilum), a hybrid of two distinct cichlid fish, is a popular ornamental fish. Its red appearance, achieved through its initial black coloration fading three weeks after hatching, is a key factor in its appeal. However, some juveniles retain their black or mottled skin. Despite its popularity, the molecular mechanisms underlying these color variations remain unclear. In this study, we compared the transcriptome profiles of fading and non-fading skin, identifying 167 differentially expressed genes. Non-fading (black) fish showed 88 up-regulated genes and 79 down-regulated genes compared to those in fading (white) fish. qPCR validated a subset of these RNA-Seq results. The enrichment analysis showed that these genes are associated with melanin production, the cAMP signaling pathway, and fatty acid metabolism. Genes related to eumelanin synthesis were up-regulated, while another synthesis pathway was down-regulated. Genes in the SLC and PDE families, linked to pheomelanin synthesis, were also up-regulated. Our findings suggest that the MSH-MC1R signaling pathway, the SCF/c-kit-Ras pathway, and the pheomelanin synthesis pathway play crucial roles in determining the development of black skin. These conclusions provide a theoretical framework for further research into pigment deposition and breeding albino varieties.