Integrated transcriptomic data reveal a regulatory network for the lignin biosynthesis in Nicotiana tabacum upon drought stress

IF 1.6 3区 农林科学 Q2 AGRONOMY Genetic Resources and Crop Evolution Pub Date : 2024-09-18 DOI:10.1007/s10722-024-02149-2
Maryam Rashidifar, Hossein Askari, Ali Moghadam
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Abstract

Lignin plays a crucial role in the production of phenolic compounds in tobacco smoke that have potential health effects associated with tobacco use. A meta-analysis of RNA-seq research and analysis of Nicotiana tabacumrevealed distinctive expression patterns of the lignin biosynthetic network. Through a meta-analysis of RNA-seq data on Nicotiana tabacum under drought stress, we identified 67 differentially expressed genes (DEGs) associated with lignin biosynthesis. Notably, 17 of these DEGs were detected only through meta-analysis, and not in individual investigations. WGCNA showed 14 clusters for the meta-genes. Several TF families and regulatory factors were identified as the most likely candidate genes related to the lignin metabolic pathway. Quantitative RT-PCR analysis of eight major meta-genes in two tobacco genotypes with contrasting lignin content (NC100 – high lignin content; Burley, low lignin content) under PEG-induced drought stress showed genotype-specific responses. CAD2 and ATH12 were upregulated in NC100, while CAD2 and CCR were upregulated in Burly. Interestingly, despite overall lignin accumulation, expression levels of CCoAOMT, F5H, COMT, and ODO1 were reduced in both genotypes.Our findings highlight the complex regulation of lignin biosynthesis under drought stress and the importance of genotype-specific responses. This study demonstrates the power of meta-analysis in identifying DEGs not detected in individual investigations, enhancing our understanding of lignin metabolism in tobacco under drought conditions. The observed genotype-specific differences underscore the need for tailored approaches in studying lignin biosynthesis in various tobaccocultivars under stress.

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综合转录组数据揭示了干旱胁迫下烟草木质素生物合成的调控网络
木质素在烟草烟雾中产生酚类化合物的过程中起着至关重要的作用,而酚类化合物会对吸烟者的健康产生潜在影响。一项针对烟草的 RNA-seq 研究和分析的荟萃分析揭示了木质素生物合成网络的独特表达模式。通过对干旱胁迫下烟草的 RNA-seq 数据进行荟萃分析,我们发现了 67 个与木质素生物合成相关的差异表达基因(DEGs)。值得注意的是,这些 DEGs 中有 17 个仅在元分析中被检测到,而不是在个别研究中被检测到。WGCNA 显示了 14 个元基因群。一些 TF 家族和调控因子被确定为最有可能与木质素代谢途径相关的候选基因。在 PEG 诱导的干旱胁迫下,对两种木质素含量不同的烟草基因型(NC100--木质素含量高;Burley--木质素含量低)中的八个主要元基因进行了定量 RT-PCR 分析,结果显示了基因型特异性反应。在 NC100 中,CAD2 和 ATH12 上调,而在 Burly 中,CAD2 和 CCR 上调。有趣的是,尽管木质素总体积累,但两种基因型中 CCoAOMT、F5H、COMT 和 ODO1 的表达水平都降低了。这项研究证明了荟萃分析在识别单个研究未检测到的 DEGs 方面的能力,从而加深了我们对干旱条件下烟草木质素代谢的了解。观察到的基因型特异性差异突出表明,在研究各种烟草栽培品种在胁迫条件下的木质素生物合成时,需要采用有针对性的方法。
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来源期刊
Genetic Resources and Crop Evolution
Genetic Resources and Crop Evolution 农林科学-农艺学
CiteScore
4.10
自引率
10.00%
发文量
178
审稿时长
3 months
期刊介绍: Genetic Resources and Crop Evolution is devoted to all aspects of plant genetic resources research. It publishes original articles in the fields of taxonomical, morphological, physiological, biochemical, genetical, cytological or ethnobotanical research of genetic resources and includes contributions to gene-bank management in a broad sense, that means to collecting, maintenance, evaluation, storage and documentation. Areas of particular interest include: -crop evolution -domestication -crop-weed relationships -related wild species -history of cultivated plants including palaeoethnobotany. Genetic Resources and Crop Evolution also publishes short communications, e.g. newly described crop taxa, nomenclatural notes, reports of collecting missions, evaluation results of gene-bank material etc. as well as book reviews of important publications in the field of genetic resources. Every volume will contain some review articles on actual problems. The journal is the internationalized continuation of the German periodical Die Kulturpflanze, published formerly by the Institute of Plant Genetics and Crop Plant Research at Gatersleben, Germany. All contributions are in the English language and are subject to peer reviewing.
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