Elsevier

Genomics

Volume 109, Issues 3–4, July 2017, Pages 258-264
Genomics

Identification and characterization of known and novel microRNAs in three tissues of Chinese giant salamander base on deep sequencing approach

https://doi.org/10.1016/j.ygeno.2017.04.007Get rights and content
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Highlights

  • We identified three libraries of A. davidianus miRNAs. A total of 553 known and 44 novel miRNAs were identified from liver, spleen and muscle, with several miRNAs shared between tissues.

  • Differentially expressed miRNAs were identified.

  • Select eight miRNAs expression level were reconfirmed with qRT-PCR technology.

  • This is the first comprehensive study of miRNAs in A. davidianus.

Abstract

MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although animal miRNAs have been extensively studied in model systems, less is known in other animal with limited genome sequence data, including Chinese giant salamander (Andrias davidianus). The identification of the full repertoire of miRNAs expressed in the liver, spleen and muscle of A. davidianus would significantly increase our understanding for physiological function of A. davidianus, in this ancient and endangered urodele amphibian. In this study, three independent small RNA libraries were constructed from the liver, spleen and muscle of A. davidianus. The libraries were subjected to high-throughput sequencing by using the Illumina deep sequencing. As a result, a total of 12,831,239, 13,592,195 and 9,887,531 raw reads representing 2,240,771, 1,363,266 and 1,964,252 clean reads per library were obtained separately. Through bioinformatics analysis, we identified total of 553 known miRNAs and 44 putative novel miRNAs in our small RNA dataset from liver, spleen and muscle tissues. Five known miRNAs (gga-miR-10a-5p, pma-miR-29d-5p, aca-miR-338-3p, hsa-miR-455-3p and ssa-miR-2184-5p_R-1) and three novel miRNAs (PC-5p-891_1763, PC-5p-32538_50 and PC-3p-33645_48) showed different expression in eight different tissues as revealed by stem-loop qPCR analysis. This study characterized the miRNA of A. davidianus for the first time, which provides an opportunity for further understanding of miRNA regulation function in A. davidianus ranked as living fossils.

Keywords

Deep sequencing
Andrias davidianus
miRNAs
Differentially expression

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