Prediction of microRNAs in Pseudomonas syringae pv. tomato DC3000 and their potential target prediction in Solanum lycopersicum

Abstract

MicroRNAs (miRNAs) regulate gene expression at the post-transcription level. It is a well explored field of non-coding RNAs, except in bacterial genomes. Here we investigated the transcriptome of Pseudomonas syringae pv. tomato DC3000 (PsPto) for the identification of non-coding RNAs. A total of 52 putative mature miRNAs were identified from the genome of PsPto using miRDeep* and CID-miRNA methods. One PsPto miRNA shared a common sequence with the reported miRNAs of E. coli DH10B, and two PsPto miRNAs shared a common sequence with the reported miRNAs of S. mutans ATCC 25175. Seven putative sequence homology miRNAs were found in different Thalassospira species. The present study provides the inclusive list of computationally identified miRNAs and filled up the existing knowledge gap on the presence of miRNAs in the PsPto genome. Moreover, a total of 93 target genes in tomato (Solanum lycopersicum) were identified for 46 PsPto miRNAs by using psRNATarget. The majority of the targets are transcription factors that play important roles in tomato development, including stress response, structural component, development, and metabolism. The results of this study will help to explain the function of miRNAs in S. lycopersicum and are intended to set the basis for further studies into PsPto miRNAs. Overall, this study can initiate further study on miRNA in regulating the growth and development of the important food tomato.