Dynamic Analysis of microRNAs from Different Life Stages of Rhipicephalus microplus (Acari: Ixodidae) by High-Throughput Sequencing

MicroRNAs (miRNAs), which are small, noncoding RNA molecules, play an important regulatory role in gene expression at the posttranscriptional level. Relatively limited knowledge exists on miRNAs in Rhipicephalus microplus ticks in China; however, understanding the physiology of miRNA functions and expression at different developmental stages is important. In this study, three small RNA libraries were constructed for R. microplus eggs, larvae, and female adults; miRNAs were detected during these developmental stages by high-throughput sequencing, with 18,162,337, 8,090,736, and 11,807,326 clean reads, respectively. A total of 5132 known miRNAs and 31 novel miRNAs were identified. A total of 1736 differentially expressed miRNAs were significantly different at a p-value of <0.01; in female adults, 467 microRNAs were upregulated and 376 miRNAs downregulated compared to larval tick controls. Using larvae as controls, 218 upregulated and 203 downregulated miRNAs were detected in eggs; in eggs, 108 miRNAs were upregulated and 364 downregulated compared to female adults controls. To verify the reliability of the sequencing data, RT−qPCR was applied to compare expression levels of novel miRNAs. Some differentially expressed miRNAs are involved in developmental physiology, signal transduction, and cell-extracellular communications based on GO annotation and KEGG pathway analyses. Here, we provide a dynamic analysis of miRNAs in R. microplus and their potential targets, which has significance for understanding the biology of ticks and lays the foundation for improved understanding of miRNA functioning in the regulation of R. microplus development. These results can assist future miRNA studies in other tick species that have great significance for human and animal health.