Identification And Bioinformatics Analysis Of Microrna Genes In Five Agricultural Pests

Small RNAs are an important class of non-coding RNAs, including miRNA (microRNA), piRNA (piwi associated RNA), siRNA (small interfering RNA) and long non-coding RNA. In past decades, messenger RNA (mRNA) played major roles in molecular biology research becausse they encode proteins. Discovery of microRNA and piRNA opened a new era of noncoding RNA study. MicroRNA is one of the most important class of noncoding RNA genes, which involved in the growth of organisms, cell differentiation and apoptosis, tumor formation and occurrence of cancer and other life processes.Unfortunately, insect microRNAs has been less understood. In insect miRNA research filed, finding small RNA genes is still the important task. The traditional experimental methods is time-consuming and laborious. The deep sequencing technology provides a powerful tool to identify small RNA genes at a large-scale level. In this paper, we sequenced small RNAs of five important agricultural pests, Tryporyza incertulas (walker), Spodoptera exigua Hiibner, Plutella xylostella(L.), Nilaparvata lugens(Stal), Laodelphgax striatellus. A comprehensive pipeline was developed to discover miRNAs by comparative genomics and machine learning methods. The genome of Bombyx moriandAcyrthosiphon pisumwere used as the reference. As a result,188microRNAs were found, which has homoloies in the miRBase database.52microRNA were successfully identifed by the software mireap using the reference genome. Combining transcriptome and small RNA library data,41microRNA were successfully detected using miRDeep.To predict microRNA targets,11,5013’UTR sequences were identified from the transcriptome data by a perl script. By using miranda software,3,197targets were predicted for281miRNAs.