Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
Genomics Proteomics Bioinformatics. 2020 Jun;18(3):352-358. doi: 10.1016/j.gpb.2020.10.001. Epub 2020 Nov 4.
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.
最近发现的环状 RNA（circRNAs）及其功能特征的描述为理解基因组生物学开辟了新途径。circRNAs 被认为在多种生物学过程中发挥重要作用，但它们的确切功能仍很大程度上难以捉摸。目前，有几种方法可用于预测新型 circRNA，但几乎所有这些方法都针对动物基因组。考虑到植物和哺乳动物基因组的组织之间存在重大差异，因此需要一种特定于植物的方法来提高植物 circRNA 鉴定的有效性。在本研究中，我们提出了 CircPlant，这是一种用于探索植物 circRNAs 的集成工具，这些 circRNAs 可能作为竞争性内源 RNA（ceRNA）发挥作用，并具有潜在的功能。通过纳入几个独特的植物特异性标准，CircPlant 可以从高通量 RNA-seq 数据中准确检测植物 circRNAs。通过对来自拟南芥和水稻的模拟和真实 RNA-seq 数据集的比较测试，我们表明 CircPlant 在准确性和效率方面均优于所有评估的竞争工具。CircPlant 可在 http://bis.zju.edu.cn/circplant 上免费获取。
