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.

环状RNA（circRNA）的最新发现及其功能作用的表征为理解基因组生物学开辟了一条新途径。circRNA被认为在多种生物学过程中起着重要作用，但其精确功能仍然难以捉摸。目前，有几种方法可用于新颖的circRNA预测，但几乎所有这些方法都适用于动物基因组。考虑到植物和哺乳动物基因组组织之间的主要差异不可忽略，因此需要一种植物特异性方法来增强植物circRNA鉴定的有效性。在这项研究中，我们介绍了CircPlant，这是一种用于探索植物circRNA的集成工具，它有可能充当竞争性内源RNA（ceRNA）及其潜在功能。通过合并几个独特的植物特定标准，CircPlant可以从高通量RNA-seq数据中准确检测植物circRNA 。基于对拟南芥和稻的模拟和真实RNA-seq数据集的比较测试，我们显示CircPlant在准确性和效率上均优于所有评估的竞争工具。CircPlant可从http://bis.zju.edu.cn/circplant免费获得。