TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs

Jing Liu,Xiaonan Liu,Xuan Ma,Shanshan Liang,Siju Zhang,Weijiang Luan

doi:10.1186/s12864-021-07680-5

Abstract

BackgroundIn plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in silico prediction normally contains false positive results. In addition, many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). Creating a comprehensive and relatively high-confidence plant miRNA target database is much needed.ResultsHere, we report TarDB, an online database that collects three categories of relatively high-confidence plant miRNA targets: (i) cross-species conserved miRNA targets; (ii) degradome/PARE (Parallel Analysis of RNA Ends) sequencing supported miRNA targets; (iii) miRNA-triggered phasiRNA loci. TarDB provides a user-friendly interface that enables users to easily search, browse and retrieve miRNA targets and miRNA initiated phasiRNAs in a broad variety of plants. TarDB has a comprehensive collection of reliable plant miRNA targets containing previously unreported miRNA targets and miRNA-triggered phasiRNAs even in the well-studied model species. Most of these novel miRNA targets are relevant to lineage-specific or species-specific miRNAs. TarDB data is freely available at http://www.biosequencing.cn/TarDB.ConclusionsIn summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.

Highlights

In plants, microRNAs are pivotal regulators of plant development and stress responses
In plants, microRNAs are endogenous ~ 21 nucleotide non-coding RNAs, which are loaded into ARGONAUTE1 (AGO1) forming RNA-induced silencing complex (RISC) to direct RNA cleavage or translational repression of target transcripts [1,2,3,4,5]
The miRNA target data deposited at TarDB consist of three categories: cross-species conserved miRNA targets, degradome/PARE-seq supported miRNA targets and miRNA-triggered phasiRNAs

Summary

Introduction

MicroRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; in silico prediction normally contains false positive results. Many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). MicroRNAs (miRNAs) are endogenous ~ 21 nucleotide (nt) non-coding RNAs, which are loaded into ARGONAUTE1 (AGO1) forming RNA-induced silencing complex (RISC) to direct RNA cleavage or translational repression of target transcripts [1,2,3,4,5]. To fully understand miRNA-target RNA interactions, miRNA target prediction and validation become vital. Bioinformatics tools or web servers such as Targetfinder, psRNATarget, psRobot, comTAR, TAPIR and TarHunter have been developed to predict miRNA targets in plants [14,15,16,17,18,19]. The detailed protocols of implementing these tools were recently reviewed [20]

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Discussion

Conclusion