Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)

Abstract

Teleosts have more types of chromatophores than other vertebrates and the genetic basis for pigmentation is highly conserved among vertebrates. Therefore, teleosts are important models to study the mechanism of pigmentation. Although functional genes and genetic variations of pigmentation have been studied, the mechanisms of different skin coloration remains poorly understood. The koi strain of common carp has various colors and patterns, making it a good model for studying the genetic basis of pigmentation. We performed RNA-sequencing for red skin and white skin and identified 62 differentially expressed genes (DEGs). Most of them were validated with RT-qPCR. The up-regulated DEGs in red skin were enriched in Kupffer’s vesicle development while the up-regulated DEGs in white skin were involved in cytoskeletal protein binding, sarcomere organization and glycogen phosphorylase activity. The distinct enriched activity might be associated with different structures and functions in erythrophores and iridophores. The DNA methylation levels of two selected DEGs inversely correlated with gene expression, indicating the participation of DNA methylation in the coloration. This expression characterization of red—white skin along with the accompanying transcriptome-wide expression data will be a useful resource for further studies of pigment cell biology.

Morphological Characters and Transcriptome Profiles Associated with Black Skin and Red Skin in Crimson Snapper (Lutjanus erythropterus)

“…After the GO and KEGG analyses of DTGs, the most clustered groups of DTGs were consistent with previous works about fish, like zebrafish [ 17 ], Midas cichlids [ 25 ] and common carp [ 3 , 24 , 33 ]. After the GO analysis of the DTGs, we found that most of the down-regulated genes were enriched in pathways like Glycolysis/Gluconeogenesis, Citrate cycle, Oxidative phosphorylation, Cardiac muscle contraction and Proteasome, which implied the participation of these pathways in the formation of red skin.…”

“…The identified DTGs between the two color skins will not only help us to understand the molecular mechanism of skin color differences, but also provide us valuable gene information for exploring the relevance of speciation and pigmentation in this species. Compared to the recent RNA-Seq research on common carp skin [ 33 ], more DTGs were found in our study. The first reason might be less use of analysis technology, as the aim of this study is to identify a large number of candidate genes for subsequent analysis, only one conventional technology DEGseq [ 34 ] was used to identify the DTGs.…”

Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing

“…8 . Many genes in the melanogenesis pathway have been linked to skin color in Koi carp, including Mc1r , Msh , Mitf , kit oncogene ( KIT ), and Tyr [ 39 ]. We identified Mc1r as a target of miR-200b , miR-206 , miR-196a , and novel-miRn1185 .…”

De novo Transcriptome Assembly of the Clown Anemonefish (Amphiprion percula): A New Resource to Study the Evolution of Fish Color

“…Previous research has shown that smooth muscle proteins are a cellular component of the chromatophores that are responsible for fish skin coloration and suggested that they may control the movement of intracellular bodies (melanophores, xanthophores, and erythrophores) within the chromatophore (Meyer-Rochow et al, 2001). The over-representation of muscle related GO terms in orange tissue might suggest greater motility control of the intracellular bodies in this skin type (Li et al, 2015), which might facilitate changes FIGURE 3 | Gene ontology (GO) categories significantly enriched for both pairwise color comparisons for each epidermal tissue by "cellular component" (CC) using Mann-Whitney U tests based on ranking of signed log p-values computed using EdgeR. Results indicate the GO domain (CC), the subdomains discussed in text ("muscle" and "extracellular matrix"), the specific GO terms, and enrichment direction observed consistently in each epidermal tissue color.…”