Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Qi, Huan, Guo, Xiaokun, Wang, Tianpeng, Zhang, Ziding
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9031537/
https://www.ncbi.nlm.nih.gov/pubmed/35456896
http://dx.doi.org/10.3390/ijms23084079
_version_ 1784692414339874816
author Qi, Huan
Guo, Xiaokun
Wang, Tianpeng
Zhang, Ziding
author_facet Qi, Huan
Guo, Xiaokun
Wang, Tianpeng
Zhang, Ziding
author_sort Qi, Huan
collection PubMed
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 Arabidopsis in response to heat stress.
format Online
Article
Text
id pubmed-9031537
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-90315372022-04-23 ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data Qi, Huan Guo, Xiaokun Wang, Tianpeng Zhang, Ziding Int J Mol Sci Article 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. MDPI 2022-04-07 /pmc/articles/PMC9031537/ /pubmed/35456896 http://dx.doi.org/10.3390/ijms23084079 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Qi, Huan
Guo, Xiaokun
Wang, Tianpeng
Zhang, Ziding
ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data
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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9031537/
https://www.ncbi.nlm.nih.gov/pubmed/35456896
http://dx.doi.org/10.3390/ijms23084079
work_keys_str_mv AT qihuan astoolaneasytousetooltoaccuratelyidentifyalternativesplicingeventsfromplantrnaseqdata
AT guoxiaokun astoolaneasytousetooltoaccuratelyidentifyalternativesplicingeventsfromplantrnaseqdata
AT wangtianpeng astoolaneasytousetooltoaccuratelyidentifyalternativesplicingeventsfromplantrnaseqdata
AT zhangziding astoolaneasytousetooltoaccuratelyidentifyalternativesplicingeventsfromplantrnaseqdata