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Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
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Discovery of replicating circular RNAs by RNA-seq and computational algorithms
Zhixiang Zhang1, Shuishui Qi2, Nan Tang2
1School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
Plos Pathogens
|December 16, 2014
Summary
A new computational tool, PFOR2, accelerates the discovery of circular RNAs, including novel viroids like Grapevine latent viroid (GLVd) and Apple hammerhead viroid-like RNA (AHVd-like RNA). This advancement overcomes limitations of previous methods, enabling broader identification of these plant pathogens.
Area of Science:
- * Molecular Biology
- * Plant Pathology
- * Bioinformatics
Background:
- * Replicating circular RNAs, such as viroids and satellite RNAs, are significant plant pathogens and viral modulators.
- * Traditional methods for discovering these subviral agents are technically challenging and time-consuming, leading to a slow discovery rate.
- * Previous computational approaches like PFOR were limited by speed and inability to detect certain types of circular RNAs.
Purpose of the Study:
- * To develop an improved computational tool for the efficient and comprehensive discovery of replicating circular RNAs.
- * To overcome the limitations of existing methods in detecting diverse subviral pathogens.
- * To identify novel circular RNAs in plant samples.
Main Methods:
- * Development of PFOR2, a C++ based computational program utilizing parallel programming for significantly increased speed (3-8x faster than PFOR).
- * Incorporation of a new algorithm into PFOR2 to enable circular RNA identification from deep sequencing of long RNAs, in addition to small RNAs.
- * Analysis of small RNA libraries from grapevine and apple plants using PFOR2.
Main Results:
- * Discovery of Grapevine latent viroid (GLVd), proposed as a new species in the Apscaviroid genus, which initiates independent infection.
- * Identification of Apple hammerhead viroid-like RNA (AHVd-like RNA), encoding a biologically active hammerhead ribozyme and not associated with known apple viruses.
- * Demonstrated the enhanced capability of PFOR2 in discovering novel circular RNAs.
Conclusions:
- * PFOR2 represents a significant advancement in the discovery of replicating circular RNAs, offering improved speed and broader detection capabilities.
- * The developed computational algorithms have broad potential for discovering novel circular RNAs across various organisms, including plants, invertebrates, and vertebrates.
- * This work facilitates a more comprehensive understanding and surveillance of subviral pathogens and their roles in disease.
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