Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing.
Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing.
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DOI：
10.1186/s12864-018-5189-5
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发表时间：
2018-10-29
期刊：
影响因子：
4.4
通讯作者：
Dong Z
中科院分区：
文献类型：
--
作者：
Luo M;Wang L;Zhu W;Fu J;Song F;Fang M;Dong J;Dong Z
微小RNA（microRNAs，miRNAs）是一种内源性的小分子（21-25个核苷酸）非编码RNA，在许多生物学过程中发挥重要作用。锦鲤具有多样的颜色模式，使其成为研究色素遗传学的理想对象。然而，miRNAs对锦鲤肤色调节和变异的影响知之甚少。本文利用Illumina测序技术对锦鲤三种主要肤色的小分子RNA（sRNA）进行了分析。结果显示，在黑色、红色和白色文库中，分别有330、397和335个保守的miRNAs（属于81个家族）和340、353和351个候选miRNAs。共鉴定了164个差异表达的miRNA（DEMs）和14个重叠的DEMs，包括miR-196 a、miR-125 b、miR-202、miR-205- 5 p、miR-200 b等。和Sox 10可能与色素沉着有关。用于相对定量的参考miRNAs的测定显示let-7a是最丰富的单个参考基因，let-7a和miR-26 b是最丰富的组合。这些发现为锦鲤肤色分化的分子机制提供了新的见解，并为锦鲤组织特异性miRNA丰度的未来研究提供了有价值的参考。本文的在线版本（10.1186/s12864-018-5189-5）包含补充材料，可供授权用户使用。
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. However, the influence of miRNAs on skin color regulation and variation in Koi carp is poorly understood. Herein, 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. The 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. The online version of this article (10.1186/s12864-018-5189-5) contains supplementary material, which is available to authorized users.
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