CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants.
10.1016/j.gpb.2020.10.001
- Author:
Peijing ZHANG
1
;
Yongjing LIU
1
;
Hongjun CHEN
1
;
Xianwen MENG
1
;
Jitong XUE
2
,
3
;
Kunsong CHEN
4
,
5
;
Ming CHEN
2
,
6
Author Information
1. Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
2. Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
3. James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
4. Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
5. The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China.
6. James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address: mchen@zju.edu.cn.
- Publication Type:Research Support, Non-U.S. Gov't
- Keywords:
Circular RNA;
Identification;
MicroRNA;
Plant;
RNA-seq
- MeSH:
Arabidopsis/metabolism*;
Oryza/metabolism*;
RNA, Circular/metabolism*;
RNA, Plant/metabolism*;
Sequence Analysis, RNA/methods*
- From:
Genomics, Proteomics & Bioinformatics
2020;18(3):352-358
- CountryChina
- Language:English
-
Abstract:
The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
