Introduction

Circular RNA (circRNA) is a group of endogenous non-coding RNAs, which are widely expressed in various tissues and have functional implications in cellular process. Due to the distinct differences in alternative splicing and organization of genomes in plant and mammal, a sensitive and accurate tool especially for detecting plant circRNA is needed.

We have presented a comprehensive tool named CircPlant for exploration of potential circRNAs and their interactions with miRNAs, combined with modified CIRI2 and TargetFinder as extensions. Besides containing plant-specific core algorithms, CircPlant has more user-friendly operations with fewer dependencies. By searching for circRNA-miRNA interactions, it allows the discovery of circRNA regulatory roles and helps to decipher the mystery of plant circRNA.

Implementation

Based on rRNA depleted total RNA or poly(A) depleted RNA sequencing data, CircPlant enables users to detect plant circRNAs with miRNA interactions. The figure illustrates the workflow of CircPlant, which is composed of three modules as below:

• Module 1: candidate circRNA identification

• Module 2: circRNA filter

• Module 3: circRNA-miRNA interaction prediction

The CircPlant package was developed in Perl by combining the core algorithm of CIRI2 and TargetFinder, BWA-MEM for reads mapping. The package has been tested on Linux platforms like Ubuntu 14.04.