The Evaluation Of Plant MiRNA Analysis Software And The Roles Of MiRNA In DNA Damage Response

With the development of the next-generation sequencing (NGS) techniques, more and more software tools were developed to detect miRNA from small RNA deep-sequencing data. An overall evaluation of these tools in plants is lacking. In the process of plant DNA replication, DNA is damaged by various agents. There are lots of reports about the roles of animal miRNA in DNA damage response (DDR), but less in plant.Here, we evaluate the sensitivity, false positive rate (FPR) and accuracy of five software tools for plants by using both simulated data and experimental data. We found that the matched pattern of a tool determined the efficiency. While software with higher sensitivity, lower FPR and higher accuracy is needed to be developed to identify known miRNA and to predict novel miRNA. Among these five software tools, miRNAkey has both high sensitivity, low FPR and the high accuracy. We chose miRNAkey to analysis a small RNA sequencing data from DNA double-strand breaks. We identified five miRNAs and predicted their30targets. After analyzing the molecular function and biological process of the predicted targets, we made a conjecture about the role of those plant miRNAs in DDR. miR399a may regulate the ubiquitination of H2A in the process of DNA double-strand break repair, miR852may regulate the cell cycle. Further research is needed to detect the roles of the rest miRNAs.