Comprehensive Transcriptome Analysis of Different Skin Colors to Evaluate Genes Related to the Production of Pigment in Celestial Goldfish

Skin color is an important phenotypic feature of vertebrate fitness under natural conditions. Celestial goldfish, a common goldfish breed in China, mainly shows three kinds of skin colors including white, yellow and brown. However, the molecular genetic basis of this phenotype is still unclear. In this study, high-throughput sequencing was carried out on the back skin tissues of celestial goldfish with different skin colors. About 58.46 Gb of original data were generated, filtered and blasted, and 74,297 mRNAs were obtained according to the reference transcriptome. A total of 4653 differentially expressed genes were screened out among the brown, yellow and white groups, and the expression of melanogenesis related genes in brown goldfish was significantly higher than the other two groups. There are 19 common differentially expressed genes among three groups, of which eight genes are related to pigment production, including tyrp1a, slc2a11b, mlana, gch2, loc113060382, loc113079820, loc113068772 and loc113059134. RT-qPCR verified that the expression patterns of randomly selected differentially expressed transcripts were highly consistent with those obtained by RNA sequencing. GO and KEGG annotation revealed that these differentially expressed genes were mostly enriched in pathways of the production of pigment, including melanogenesis, tyrosine metabolism, Wnt signaling pathway, MAPK signaling pathway etc. These results indicated that the external characteristics of goldfish are consistent with the analysis results at transcriptome level. The results of this study will lay a foundation for further study on the expression characteristics and gene network analysis of pigment related genes.