A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution

Alternative splicing (AS) expands the transcriptome diversity by selectively splicing exons and introns from pre-mRNAs to generate different protein isoforms. This mechanism is widespread in eukaryotes and plays a crucial role in development, environmental adaptation, and stress resistance. In this...

Full description

Saved in:
Bibliographic Details
Main Authors: Shizhou Yu, Jufen Wan, Tenghang Xu, Jie Zhang, Linggai Cao, Jie Liu, Hongfeng Liu, Xueliang Ren, Zhixiao Yang
Format: Article
Language:English
Published: Frontiers Media S.A. 2025-02-01
Series:Frontiers in Plant Science
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fpls.2025.1500654/full
Tags: Add Tag
No Tags, Be the first to tag this record!
_version_ 1825206754278899712
author Shizhou Yu
Jufen Wan
Jufen Wan
Tenghang Xu
Tenghang Xu
Jie Zhang
Linggai Cao
Jie Liu
Hongfeng Liu
Xueliang Ren
Zhixiao Yang
author_facet Shizhou Yu
Jufen Wan
Jufen Wan
Tenghang Xu
Tenghang Xu
Jie Zhang
Linggai Cao
Jie Liu
Hongfeng Liu
Xueliang Ren
Zhixiao Yang
author_sort Shizhou Yu
collection DOAJ
description Alternative splicing (AS) expands the transcriptome diversity by selectively splicing exons and introns from pre-mRNAs to generate different protein isoforms. This mechanism is widespread in eukaryotes and plays a crucial role in development, environmental adaptation, and stress resistance. In this study, we collected 599 tobacco RNA-seq datasets from 35 projects. 207,689 transcripts were identified in this study, of which 35,519 were annotated in the reference genome, while 172,170 transcripts were newly annotated. Additionally, tissue-specific analysis revealed 4,585 transcripts that were uniquely expressed in different tissues, highlighting the complexity and specialization of tobacco gene expression. The analysis of AS events (ASEs) across different tissues showed significant variability in the expression levels of ASE-derived transcripts, with some of these transcripts being associated with stress resistance, such as the geranyl diphosphate synthase (GGPPS). Moreover, we identified 21,763 splicing quantitative trait locus (sQTLs), which were enriched in genes involved in biological processes such as histone acetylation. Furthermore, sQTLs involved genes related to plant hormone signal transduction, terpenoid backbone biosynthesis, and other resistance pathways. These findings not only reveal the diversity of gene expression in tobacco but also provide new insights and strategies for improving tobacco quality and resistance.
format Article
id doaj-art-d7ea7341767d42b69b908b63e59574bc
institution Kabale University
issn 1664-462X
language English
publishDate 2025-02-01
publisher Frontiers Media S.A.
record_format Article
series Frontiers in Plant Science
spelling doaj-art-d7ea7341767d42b69b908b63e59574bc2025-02-07T06:49:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-02-011610.3389/fpls.2025.15006541500654A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolutionShizhou Yu0Jufen Wan1Jufen Wan2Tenghang Xu3Tenghang Xu4Jie Zhang5Linggai Cao6Jie Liu7Hongfeng Liu8Xueliang Ren9Zhixiao Yang10Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaMolecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaState Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, ChinaMolecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaCollege of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, ChinaMolecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaMolecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaMolecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaGuiyang Branch Company of Guizhou Tobacco Company, Guiyang, ChinaMolecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaMolecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, ChinaAlternative splicing (AS) expands the transcriptome diversity by selectively splicing exons and introns from pre-mRNAs to generate different protein isoforms. This mechanism is widespread in eukaryotes and plays a crucial role in development, environmental adaptation, and stress resistance. In this study, we collected 599 tobacco RNA-seq datasets from 35 projects. 207,689 transcripts were identified in this study, of which 35,519 were annotated in the reference genome, while 172,170 transcripts were newly annotated. Additionally, tissue-specific analysis revealed 4,585 transcripts that were uniquely expressed in different tissues, highlighting the complexity and specialization of tobacco gene expression. The analysis of AS events (ASEs) across different tissues showed significant variability in the expression levels of ASE-derived transcripts, with some of these transcripts being associated with stress resistance, such as the geranyl diphosphate synthase (GGPPS). Moreover, we identified 21,763 splicing quantitative trait locus (sQTLs), which were enriched in genes involved in biological processes such as histone acetylation. Furthermore, sQTLs involved genes related to plant hormone signal transduction, terpenoid backbone biosynthesis, and other resistance pathways. These findings not only reveal the diversity of gene expression in tobacco but also provide new insights and strategies for improving tobacco quality and resistance.https://www.frontiersin.org/articles/10.3389/fpls.2025.1500654/fullNicotiana tabacumASEtissue-specific transcriptstress responseSQTL
spellingShingle Shizhou Yu
Jufen Wan
Jufen Wan
Tenghang Xu
Tenghang Xu
Jie Zhang
Linggai Cao
Jie Liu
Hongfeng Liu
Xueliang Ren
Zhixiao Yang
A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution
Frontiers in Plant Science
Nicotiana tabacum
ASE
tissue-specific transcript
stress response
SQTL
title A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution
title_full A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution
title_fullStr A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution
title_full_unstemmed A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution
title_short A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution
title_sort gene expression atlas of nicotiana tabacum across various tissues at transcript resolution
topic Nicotiana tabacum
ASE
tissue-specific transcript
stress response
SQTL
url https://www.frontiersin.org/articles/10.3389/fpls.2025.1500654/full
work_keys_str_mv AT shizhouyu ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jufenwan ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jufenwan ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT tenghangxu ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT tenghangxu ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jiezhang ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT linggaicao ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jieliu ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT hongfengliu ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT xueliangren ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT zhixiaoyang ageneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT shizhouyu geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jufenwan geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jufenwan geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT tenghangxu geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT tenghangxu geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jiezhang geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT linggaicao geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT jieliu geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT hongfengliu geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT xueliangren geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution
AT zhixiaoyang geneexpressionatlasofnicotianatabacumacrossvarioustissuesattranscriptresolution