Abstract
MicroRNAs (miRNAs) are non-coding small RNA of approximately 22 nt in length. They are considered as key regulators for gene expression at the post-transcriptional level and play an important role in the regulation of many fundamental biological processes. Andrias davidianus, as one of the largest amphibian on earth, may represent the transitional type of animal from aquatic to terrestrial life, but so far, no miRNA has been identified in the species. In this study, Illumina deep sequencing was used for high-throughput analysis of miRNAs in a pooled small RNA library isolated from eight tissues sample of A. davidianus including the spleen, liver, muscle, kidney, skin, testis, gut, and heart. In total, 6,213,146 reads were obtained, 5,962,175 of which were related to 143 unique miRNAs, including 140 conserved and three novel A. davidianus-specific miRNAs. Among them, seven conserved miRNAs and one novel miRNA were selected to validate their expression pattern by stem-loop qRT-PCR. Moreover, 4700 potential target genes were predicted for 143 A. davidianus miRNAs; GO enrichment analysis and KEGG pathway showed that most of the targets are involved in diverse biological processes including ubiquitin-mediated proteolysis, FOXO signaling pathway, tight junction, and spliceosome. This study provides the first large-scale identification and characterization of A. davidianus miRNAs, and predicted their potential target genes; it will lay a valuable foundation for future understanding the role of these miRNAs on regulating diverse biological processes.
Highlights
MicroRNAs are a class of genome-encoded small RNAs with approximately 22 nt in length, that are abundant in most metazoans, plant, fungi, protists, and even in viruses (Lin et al 2009; Li et al 2010b; Sun et al 2012; Mu et al 2015; Chen et al 2016; Huang and Evans 2016)
Illumina deep sequencing was used for highthroughput analysis of miRNAs in a pooled small RNA library isolated from eight tissues sample of A. davidianus including the spleen, liver, muscle, kidney, skin, testis, gut, and heart
4700 potential target genes were predicted for 143 A. davidianus miRNAs; GO enrichment analysis and KEGG pathway showed that most of the targets are involved in diverse biological processes including ubiquitin-mediated proteolysis, FOXO signaling pathway, tight junction, and spliceosome
Summary
MicroRNAs (miRNAs) are a class of genome-encoded small RNAs with approximately 22 nt in length, that are abundant in most metazoans, plant, fungi, protists, and even in viruses (Lin et al 2009; Li et al 2010b; Sun et al 2012; Mu et al 2015; Chen et al 2016; Huang and Evans 2016). One of the two strands of the miRNA will be assembled with the RNA-induced silencing complex These mature miRNAs can regulate the expression of target genes by binding to the coding regions or untranslated regions (Siomi and Siomi 2010). In the evolution history of vertebrates, the Chinese giant salamander occupies a seat at the phylogenetic and species evolution process which is representing a transitional form that links the aquatic animals to terrestrial organisms. This species has an important scientific value. We performed the first deep sequencing study of the miRNA population in A. davidianus, and identified 143 miRNAs, and predicted their gene targets; this information will be helpful for understanding of miRNA populations in A. davidianus, and lay a solid foundation for further functional studies of these miRNAs
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