Abstract
BackgroundMicroRNAs (miRNAs) are endogenous, small (21–25 nucleotide), non-coding RNAs that play important roles in numerous biological processes. Koi carp exhibit diverse color patterns, making it an ideal subject for studying the genetics of pigmentation. However, the influence of miRNAs on skin color regulation and variation in Koi carp is poorly understood.ResultsHerein, we performed small RNA (sRNA) analysis of the three main skin colors in Koi carp by Illumina sequencing. The results revealed 330, 397, and 335 conserved miRNAs (belonging to 81 families) and 340, 353, and 351 candidate miRNAs in black, red, and white libraries, respectively. A total of 164 differentially expressed miRNAs (DEMs) and 14 overlapping DEMs were identified, including miR-196a, miR-125b, miR-202, miR-205-5p, miR-200b, and etc. Target prediction and functional analysis of color-related miRNAs such as miR-200b, miR-206, and miR-196a highlighted putative target genes, including Mitf, Mc1r, Foxd3, and Sox10 that are potentially related to pigmentation. Determination of reference miRNAs for relative quantification showed that let-7a was the most abundant single reference gene, and let-7a and miR-26b was the most abundant combination.ConclusionsThe findings provide novel insight into the molecular mechanisms determining skin color differentiation in Koi carp, and serve as a valuable reference for future studies on tissue-specific miRNA abundance in Koi carp.
Highlights
MicroRNAs are endogenous, small (21–25 nucleotide), non-coding RNAs that play important roles in numerous biological processes
The Melanocortin receptor 1 (Mc1r) gene is a key factor involved in the production of pheomelanin and eumelanin in melanocytes, and we found that it is targeted by miR-200a, miR-200b, and miR-206, and miR-206 presented up-regulated in black skins compared with red and white skins suggested that it played important roles in pigmentation in Koi carp
Our findings provide fundamental information on the expression of conserved and potential novel miRNAs in Koi carp skin, and identified differentially expressed miRNAs (DEMs) and their respective target genes that may be related to skin color
Summary
MicroRNAs (miRNAs) are endogenous, small (21–25 nucleotide), non-coding RNAs that play important roles in numerous biological processes. Koi carp exhibit diverse color patterns, making it an ideal subject for studying the genetics of pigmentation. Unlike the slow rate of phenotypic changes occurring in wild populations, the rapid establishment of diverse colors and coloration patterns under artificial selection makes Koi carp an ideal subject for studying the genetics of pigmentation [2]. Determination of skin color is a complicated process in fish, linked to various cellular, genetic, nutritional, MicroRNAs (miRNAs) are single-stranded, non-coding, highly-conserved 19–24 nucleotides (nt) molecules that regulate gene expression at the post-transcriptional level by directly targeting RNA-inducing silencing complex (RISC) to cognate messenger RNA targets [7, 8]. In white alpaca (WA) and brown alpaca (BA) skin, deep sequencing identified 35 and 13 conserved differentially expressed miRNAs (DEMs), indicating potential functions in coat skin color regulation [16]. The molecular and cellular mechanisms regulating skin color variation in fish, especially a variety of colors appeared on a single fish, such as Koi carp (Fig. 1), remain poorly understood
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