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

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5189-5) contains supplementary material, which is available to authorized users.

MicroRNA-206 Regulation of Skin Pigmentation in Koi Carp (Cyprinus carpio L.)

“…Animals' coloration and their pattern is an important model to excavate the genetic mechanisms that determine phenotype (Joanna et al, 2010). In this study, we mainly focused on the miR-206 functional studies based on previous small RNA sequencing results (Luo et al, 2018). Firstly, we analyzed its temporal and spatial expression pattern to gain insight into the functions.…”

“…Other genes, such as tyrosinase-related protein-1 (Tyrp1) and dopachrome tautomerase (Dct or Tyrp2), primarily regulate the eumelanin pathway (Braasch et al, 2009). Interestingly, we also identified some important miRNAs and mRNAs on black, white, and red skin of koi carp, which involved in the cAMP signaling, melanogenesis, and tyrosine metabolism pathway through Illumina sequencing (Luo et al, 2018;Luo et al, 2019). Therefore, it is necessary to further excavate the specific relationship between the coding and non-coding RNAs, e.g.…”

“…Yan et al identified the miR-429 act as a crucial role in skin pigmentation by targeting Foxd3 3'-untranslated (3'-UTR) region and silencing its expression in vivo would repress the transcription level of Mitf and its downstream genes (Yan et al, 2013). In our previous study, we have identified 164 differentially expressed miRNAs (DEMs) and 14 overlapping including miR-206 on different skin colors (black, red, and white) through Illumina sequencing in koi carp (Luo et al, 2018). However, miRNAs specific regulation mechanisms related to skin color differentiation in koi carp remains unclear.…”

Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

“…In our previous study, we identified important miRNAs (e.g. miR-196a , miR-125b , miR-200b and miR-206 ) that influence pigmentation and differentiation in the three main skin colors [23]. Despite an abundance of literature on tissue-specific expression patterns and functions of mRNAs and miRNAs in fish, evidence for tissue-restricted expression of lncRNAs is limited.…”

“…In our previous study, we performed small RNA sequencing (sRNA-Seq) on three skin colors (black, white and red) in Koi carp using Illumina sequencing. We screened 164 differentially expressed miRNAs and identified several key miRNAs related to pigment regulation including miR-196a , miR-200b , miR-125b and miR-202 [23]. In the present study, we conducted a high-throughput sequencing strategy to screen expression of lncRNAs and mRNAs in these three skin colors.…”