ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data.
ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data.
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DOI：
10.3390/ijms23084079
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发表时间：
2022-04-07
影响因子：
5.6
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Qi H;Guo X;Wang T;Zhang Z
选择性剪接（AS）是真核生物中一种重要的共转录调控机制。植物RNA-Seq数据的积累为研究植物AS事件的全球格局提供了前所未有的机会。然而，大多数现有的AS识别工具最初是为动物设计的，它们在植物中的表现并没有严格的基准。在这项工作中，我们开发了一个简单易用的生物信息学工具ASTool，用于从植物RNA-Seq数据中检测AS事件。ASTool作为一种基于外显子的方法，可以检测4种主要的AS类型，包括内含子保留（IR）、外显子跳跃（ES）、5′剪接位点（A5 SS）和3′剪接位点（A3 SS）。与现有的工具相比，ASTool在模拟RNA-Seq数据中测试时显示出良好的性能，在大多数情况下，召回率和准确率都超过95%。此外，ASTool在模拟或真实的植物RNA-Seq数据中的检测结果与现有工具的检测结果一致，具有较强的计算速度。考虑到IR是植物中最主要的AS类型，ASTool允许基于已知剪接位点检测和可视化新的IR事件。为了充分展示ASTool的功能，我们还提供了ASTool在拟南芥热胁迫响应的真实的RNA-Seq数据处理中的应用实例。
Alternative splicing (AS) is an essential co-transcriptional regulatory mechanism in eukaryotes. The accumulation of plant RNA-Seq data provides an unprecedented opportunity to investigate the global landscape of plant AS events. However, most existing AS identification tools were originally designed for animals, and their performance in plants was not rigorously benchmarked. In this work, we developed a simple and easy-to-use bioinformatics tool named ASTool for detecting AS events from plant RNA-Seq data. As an exon-based method, ASTool can detect 4 major AS types, including intron retention (IR), exon skipping (ES), alternative 5′ splice sites (A5SS), and alternative 3′ splice sites (A3SS). Compared with existing tools, ASTool revealed a favorable performance when tested in simulated RNA-Seq data, with both recall and precision values exceeding 95% in most cases. Moreover, ASTool also showed a competitive computational speed and consistent detection results with existing tools when tested in simulated or real plant RNA-Seq data. Considering that IR is the most predominant AS type in plants, ASTool allowed the detection and visualization of novel IR events based on known splice sites. To fully present the functionality of ASTool, we also provided an application example of ASTool in processing real RNA-Seq data of Arabidopsis in response to heat stress.
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