Abstract
BackgroundCrucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes and partial DNA methylation sites were obtained from red crucian carp (RCC) and white crucian carp (WCC). Here, we show significant differences in mRNA expression and DNA methylation sites between skin tissues of RCC and WCC.ResultsTotals of 3434 and 3683 unigenes had significantly lower and higher expression in WCC, respectively, compared with unigenes expressed in RCC. Some potential genes for body color development were further identified by quantitative polymerase chain reaction, such as mitfa, tyr, tyrp1, and dct, which were down-regulated, and foxd3, hpda, ptps, and gch1, which were up-regulated. A KEGG pathway analysis indicated that the differentially expressed genes were mainly related to mitogen activated protein kinase (MAPK), Wnt, cell cycle, and endocytosis signaling pathways, as well as variations in melanogenesis in crucian carp. In addition, some differentially expressed DNA methylation site genes were related to pigmentation, including mitfa, tyr, dct, foxd3, and hpda. The differentially expressed DNA methylation sites were mainly involved in signaling pathways, including MAPK, cAMP, endocytosis, melanogenesis, and Hippo.ConclusionsOur study provides the results of comparative transcriptome and DNA methylation analyses between RCC and WCC skin tissues and reveals that the molecular mechanism of body color variation in crucian carp is strongly related to disruptions in gene expression and DNA methylation during pigmentation.
Highlights
Crucian carp is a popular ornamental strain in Asia with variants in body color
Functional enrichment analysis of annotated Unigenes Twenty four thousand nine hundred seventy one unigenes were obtained from the crucian carp skin, which annotated with Gene Ontology (GO)
We evaluated the global gene expression patterns and DNA methylation patterns in the skin of crucian carp with different coloration patterns
Summary
Crucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes and partial DNA methylation sites were obtained from red crucian carp (RCC) and white crucian carp (WCC). Some species have been used as ornamental fish, in which body color and pattern are important characteristics. Pigment cells on the body surface provide body color pigment patterns and are usually classified according to pigment composition. Fish body color is controlled by the distribution of pigment cells, such as melanocytes, xanthophores, erythrophores, and iridocytes [4,5,6]. Xanthophores and erythrophores hold carotenoids and pteridines and provide the yellow, orange and red colors of fish
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