MiRkwood: a tool for the reliable identification of microRNAs in plant genomes

Isabelle Guigon,Delphine Lanselle,Jean-Frédéric Berthelot,Sébastien Bini,Mohcen Benmounah,Hélène Touzet,Sylvain Legrand

doi:10.1186/s12864-019-5913-9

Abstract

BackgroundMicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited.ResultsHere, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data. Deep-sequencing data of Argonaute associated small RNAs showed that miRkwood is able to identify a large diversity of plant miRNAs and limits false positive predictions. Moreover, it outperforms current tools such as ShortStack and contrary to ShortStack, miRkwood provides a quality score allowing users to rank miRNA predictions.ConclusionmiRkwood is a very efficient tool for the annotation of miRNAs in plant genomes. It is available as a web server, as a standalone version, as a docker image and as a Galaxy tool: http://bioinfo.cristal.univ-lille.fr/mirkwood

Highlights

MicroRNAs play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development
Datasets To evaluate the performance of miRkwood and benchmark against ShortStack [10], a dataset composed of 6.2 million Illumina raw reads and obtained from inflorescences from A. thaliana previously published by Wang et al (2011) [23] was downloaded from the SRA-NCBI database
Analysis of predictions Pre-miRNA predictions were compared to pre-miRNAs annotated in the A. thaliana genome assembly using the “intersect” function from the Bedtools suite [28]

Summary

Introduction

MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited Since their discovery in animals and plants, microRNAs (miRNAs) have been shown to play pivotal roles in growth and development of organisms. After nuclear export of pre-miRNAs, they are cleaved into miRNA/miRNA* duplexes (miRNA* being the passenger strand) by a cytoplasmic Dicer enzyme. In plants, both steps of cleaving are performed by a single nuclear Dicer-like protein (DCL). Beside 21 nt miRNAs, as shown in A. thaliana and rice, DCL3 is capable of generating 24-nt long miRNAs (lmiRNAs) from pre-miRNAs, which are loaded into AGO4 proteins

Methods

Results

Conclusion