Identification and characterization of novel drought-responsive lncRNAs in stone apple (Aegle marmelos L.) through whole-transcriptome analysis

IF 5.4 Q1 PLANT SCIENCES Current Plant Biology Pub Date : 2024-03-06 DOI:10.1016/j.cpb.2024.100336
Kishor U. Tribhuvan , Twinkle Mishra , Simardeep Kaur , Avinash Pandey , Shashi Bhushan Choudhary , V.P. Bhadana , Sujay Rakshit , Binay K. Singh
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Abstract

Stone apple (Aegle marmelos L.) is a subtropical fruit tree of the Rutaceae family, highly valued in traditional medicine across the Indian subcontinent. We conceived this study with the objective of developing a comprehensive transcriptome dataset, identifying SSRs for marker-assisted breeding, and delineating regulators of gene expression, with a specific emphasis on non-coding RNA (ncRNA), particularly related to drought stress. To achieve this, RNA-seq was conducted using RNA pooled from various tissues, including roots, leaves, inflorescence, and developing seeds from stone apple, and the clean reads were assembled into 40,886 unigenes. Subsequently, the unigenes were categorized into gene ontology categories encompassing biological processes, molecular functions, and cellular components. Within the unigenes, we identified a total of 9174 perfect simple sequence repeats (SSRs), 2167 transcription factors (TFs) distributed among 69 families, and 415 transcription regulators (TRs) across 27 families. Additionally, 19 microRNAs (miRNAs) from 12 families, 16,811 potential long noncoding RNAs (lncRNAs), and six functional endogenous target mimics (eTMs) were detected. Analysis of lncRNA-miRNA-mRNA interactions unveiled multiple regulatory nodes, elucidating lncRNA/miRNA-driven gene expression control in stone apple. The increased co-expression of selected drought-related lncRNAs and their cognate target mRNAs supported the aforementioned findings under drought conditions. Overall, this study significantly advances our understanding of stone apple genomics and lays a foundation for future omics-based studies, thereby facilitating the deployment of climate-resilient strategies in the species.

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通过全转录组分析鉴定和表征石苹果(Aegle marmelos L.)中新型干旱响应lncRNAs
石苹果(Aegle marmelos L.)是芸香科亚热带果树,在印度次大陆的传统医药中具有很高的价值。我们构思这项研究的目的是开发一个全面的转录组数据集,确定用于标记辅助育种的 SSR,并确定基因表达的调控因子,特别强调非编码 RNA(ncRNA),尤其是与干旱胁迫相关的非编码 RNA。为此,研究人员利用从砀山苹果的根、叶、花序和发育中的种子等不同组织中收集的 RNA 进行了 RNA-seq,并将干净的读数组装成 40,886 个单基因。随后,这些单基因被归入基因本体论类别,包括生物过程、分子功能和细胞成分。在这些单基因中,我们共鉴定出 9174 个完美的简单序列重复序列(SSR)、2167 个转录因子(TFs)(分布在 69 个家族中)和 415 个转录调节因子(TRs)(分布在 27 个家族中)。此外,还检测到来自 12 个科的 19 个微小核糖核酸(miRNA)、16,811 个潜在的长非编码核糖核酸(lncRNA)和 6 个功能性内源目标模拟物(eTM)。lncRNA-miRNA-mRNA相互作用分析揭示了多个调控节点,阐明了lncRNA/miRNA驱动的石苹果基因表达调控。在干旱条件下,选定的干旱相关 lncRNA 及其同源靶 mRNA 的共表达增加,支持了上述发现。总之,这项研究极大地促进了我们对砀山苹果基因组学的了解,并为未来基于组学的研究奠定了基础,从而有助于在该物种中部署气候抗性策略。
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来源期刊
Current Plant Biology
Current Plant Biology Agricultural and Biological Sciences-Plant Science
CiteScore
10.90
自引率
1.90%
发文量
32
审稿时长
50 days
期刊介绍: Current Plant Biology aims to acknowledge and encourage interdisciplinary research in fundamental plant sciences with scope to address crop improvement, biodiversity, nutrition and human health. It publishes review articles, original research papers, method papers and short articles in plant research fields, such as systems biology, cell biology, genetics, epigenetics, mathematical modeling, signal transduction, plant-microbe interactions, synthetic biology, developmental biology, biochemistry, molecular biology, physiology, biotechnologies, bioinformatics and plant genomic resources.
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