ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data
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 designe...
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| Language: | English |
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MDPI AG
2022-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/8/4079 |
| _version_ | 1797434537529049088 |
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| author | Huan Qi Xiaokun Guo Tianpeng Wang Ziding Zhang |
| author_facet | Huan Qi Xiaokun Guo Tianpeng Wang Ziding Zhang |
| author_sort | Huan Qi |
| collection | DOAJ |
| description | 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 <i>Arabidopsis</i> in response to heat stress. |
| first_indexed | 2024-03-09T10:33:45Z |
| format | Article |
| id | doaj.art-159c19d7c23e408fac934b3f63cae58a |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T10:33:45Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-159c19d7c23e408fac934b3f63cae58a2023-12-01T21:01:43ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-04-01238407910.3390/ijms23084079ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq DataHuan Qi0Xiaokun Guo1Tianpeng Wang2Ziding Zhang3State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, ChinaState Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, ChinaAlternative 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 <i>Arabidopsis</i> in response to heat stress.https://www.mdpi.com/1422-0067/23/8/4079plantalternative splicingRNA-Seq databioinformatics |
| spellingShingle | Huan Qi Xiaokun Guo Tianpeng Wang Ziding Zhang ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data International Journal of Molecular Sciences plant alternative splicing RNA-Seq data bioinformatics |
| title | ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data |
| title_full | ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data |
| title_fullStr | ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data |
| title_full_unstemmed | ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data |
| title_short | ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data |
| title_sort | astool an easy to use tool to accurately identify alternative splicing events from plant rna seq data |
| topic | plant alternative splicing RNA-Seq data bioinformatics |
| url | https://www.mdpi.com/1422-0067/23/8/4079 |
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