Yu Shizhou, Wan Jufen, Xu Tenghang, Zhang Jie, Cao Linggai, Liu Jie, Liu Hongfeng, Ren Xueliang, Yang Zhixiao
Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, China.
Front Plant Sci. 2025 Feb 7;16:1500654. doi: 10.3389/fpls.2025.1500654. eCollection 2025.
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 (). 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.
可变剪接（Alternative splicing，AS）通过从信使核糖核酸前体（pre-mRNAs）中选择性剪接外显子和内含子来扩展转录组的多样性，从而产生不同的蛋白质异构体。这种机制在真核生物中广泛存在，在发育、环境适应和抗逆性方面发挥着关键作用。在本研究中，我们从35个项目中收集了599个烟草RNA测序数据集。本研究共鉴定出207,689个转录本，其中35,519个在参考基因组中已有注释，而172,170个转录本为新注释。此外，组织特异性分析揭示了4,585个在不同组织中特异表达的转录本，突出了烟草基因表达的复杂性和特异性。对不同组织中可变剪接事件（Alternative splicing events，ASEs）的分析表明，ASE衍生转录本的表达水平存在显著差异，其中一些转录本与抗逆性相关，例如（此处原文括号内容缺失）。此外，我们鉴定出21,763个剪接数量性状位点（splicing quantitative trait locus，sQTLs），这些位点在参与诸如组蛋白乙酰化等生物过程的基因中富集。此外，sQTLs涉及与植物激素信号转导、萜类骨架生物合成及其他抗性途径相关的基因。这些发现不仅揭示了烟草基因表达的多样性，还为提高烟草品质和抗性提供了新的见解和策略。
