PlantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.

Deblina Patra,Peter F Stadler,Gerhard Steger,Mario Fasold,Ivo Grosse,David Langenberger

doi:10.3389/fpls.2014.00708

Abstract

High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis, including quality control, read normalization, ncRNA quantification, and the prediction of putative novel ncRNAs. DARIO is one such system that so far has been focussed on animals. Here we introduce an extension of this system to plant short non-coding RNAs (sncRNAs). It includes major modifications to cope with plant-specific sncRNA processing. The current version of plantDARIO covers analyses of mapping files, small RNA-seq quality control, expression analyses of annotated sncRNAs, including the prediction of novel miRNAs and snoRNAs from unknown expressed loci and expression analyses of user-defined loci. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. The web tool links to a plant specific visualization browser to display the read distribution of the analyzed sample. The easy-to-use platform of plantDARIO quantifies RNA expression of annotated sncRNAs from different sncRNA databases together with new sncRNAs, annotated by our group. The plantDARIO website can be accessed at http://plantdario.bioinf.uni-leipzig.de/.

Highlights

Plant short non-coding RNAs (sncRNAs) from seedlings and the inflorescences have been shown to have a broad range of biological functions in the model plant Arabidopsis thaliana (Lu et al, 2005)
It represents a perfect plant miRNA pattern as expected for sncRNAs processed by a plant DCL enzyme (Kurihara and Watanabe, 2004), resulting in one functional arm in this case
The irregular patterns found as little bumps in the structure are bulge loops or internal loops present in the pre-miRNA structure, which are usual, i.e., which are a thermodynamic feature of the RNA

Summary

Introduction

Plant sncRNAs from seedlings and the inflorescences have been shown to have a broad range of biological functions in the model plant Arabidopsis thaliana (Lu et al, 2005). Approximately or perfectly double-stranded RNA (dsRNA) precursors are cut by Dicer-like (DCL) proteins into small RNA duplexes (Axtell, 2013). The small RNA duplexes can be loaded onto different classes of Argonaute (AGO) proteins present in complexes of different functions that mediate the interaction of the incorporated small RNAs with their targets. For e.g., AGO1 acts mainly in microRNA (miRNA) pathways for post-transcriptional gene silencing (PTGS) (Wang et al, 2011a). In case of miRNA duplexes, while the guide strands are incorporated into AGO1 of the RNA-induced silencing complex (RISC), the passenger strands called miRNA star (miRNA∗) are mostly degraded (Wang et al, 2011b). Small RNAs loaded onto other Argonaute-containing complexes have different functions, e.g., heterochromatin maintenance

Methods

Results

Conclusion