Development Of Bioinformatics Tools For The Discovery Of MiRNA And Its Targets In Plants

Based on the widely used technology of small RNA-seq and degradome for the identification of miRNAs and their target in plants, this thesis introduces the development of two bioinformatics tools. One is a tool for identifying miRNA-target interaction, and the other for detecting miRNA response element change caused by alternative splicing. The main research contents and results are summarized as follows:1. Based on small RNA-seq and degradome data, we developed MTide, an integrated tool for the identification of miRNA-target interaction (MTI) in plants. It consists of a modified miRdeep2 for plants application, a modified CleaveLand4 for more targets report, a Perl wrapper of TAPIR for miRNA target prediction and a gene function similarity based tool for prioritization of predicted targets from TAPIR. We added multiple threads support for the time-consuming part of all the tools. To make it possible for detecting differential expressed miRNA, we also added a module derived from DESeq. It is a powerful tool for detecting MTI in a genome-wide scale, and users can run MTide sequentially or by an integrated script in a command line environment. By searching for targets of a complete miRNAs, we can facilitate large-scale identification of miRNA targets, allowing us to discover regulatory interaction networks.2. Alternative splicing event can either create or lose the miRNA response element for the corresponding transcripts, but there is no tool existing for detecting this kind of change by now. Here, we developed STplot, an efficient tool for the identification of miRNA response element change caused by alternative splicing. It adopts a new method to reconstruct the fragmented sequence of transcript based on known gene model. After that, we analyzed the predicted miRNA-target structure and degradome signature along the gene to generate detailed information about which transcripts having strong degradome signal could be targeted by miRNA. Finally, we developed a module of automatically generating spliced t-plot in both a global and local view, which is enlarged around the center of spliced sites. All the results could help to understand the miRNA response element change caused by alternative splicing.Through the above research and tools development, I hope my studies can help the potential users to dig the MTI in a comprehensive way, expand the current understanding of the interplay between miRNA and alternative splicing, and inspire further in-depth studies on the function mechanism of miRNA.