Multidimensional analysis of long noncoding RNAs function in Solanaceae plants

IF 8.3 1区生物学 Q1 PLANT SCIENCES

New Phytologist Pub Date : 2025-06-01 DOI:10.1111/nph.70261

Wenjing Yang, Quanzi Bai, Xuan Zhang, Wen Chen, Ankang Cai, Jing Li, Xiaoyang Gao, Baolin Yao, Jiazhi Liu, Yan Li, Jianghua Chen, Changning Liu

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引用次数: 0

Abstract

Long noncoding RNAs (lncRNAs) have been gradually verified as functional regulators in plants, yet their functions remain underexplored, especially in the Solanaceae family. While substantial progress has been made in identifying lncRNAs in different Solanaceae species, systematic functional annotations are lacking. In this study, we uniformly identified and systematically characterized lncRNAs from seven Solanaceous species using large-scale strand-specific RNA-seq (ssRNA-seq). About 113 700 lncRNA genes were obtained and analyzed for their sequence, conservation, expression profile, epigenetic signals, and genetic mutants. In tomato, 97.4% of lncRNAs have been annotated with basic characteristics. Also, 25.7% of lncRNAs were further predicted to be involved in stress response, development, and metabolism. Comparisons between lncRNAs and protein-coding genes (PCGs) highlighted unique characteristics in tissue expression, stress responses, sequence composition, and epigenetic signal distribution. We shared our datasets on Solanaceous lncRNAs at http://solanaceae-lncrna-source.liu-lab.com/. Taking fruit development and ripening as an example, we further mined the data resources and predicted a total of 1158 lncRNAs associated with this process, presenting how our curated data can be utilized to discover the functions of plant lncRNAs. Overall, this study provides a comprehensive multidimensional framework for lncRNA functional research, which serves as a valuable reference for understanding lncRNA functions in other plants.

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茄科植物长链非编码rna功能的多维分析

长链非编码rna （Long noncoding rna, lncRNAs）已逐渐被证实是植物的功能调控因子，但其功能仍未被充分研究，特别是在茄科植物中。虽然在茄科不同物种中lncrna的鉴定已经取得了实质性进展，但缺乏系统的功能注释。在本研究中，我们使用大规模链特异性RNA-seq （ssRNA-seq）对7种茄属植物的lncrna进行了统一鉴定和系统表征。共获得约113700个lncRNA基因，并对其序列、保守性、表达谱、表观遗传信号和基因突变进行了分析。在番茄中，97.4%的lncrna被标注了基本特征。此外，25.7%的lncrna被进一步预测参与应激反应、发育和代谢。lncRNAs与蛋白质编码基因（PCGs）的比较突出了它们在组织表达、应激反应、序列组成和表观遗传信号分布方面的独特特征。我们在http://solanaceae-lncrna-source.liu-lab.com/分享了我们在Solanaceous lncRNAs上的数据集。以果实发育和成熟为例，我们进一步挖掘数据资源，共预测了1158个与此过程相关的lncrna，展示了如何利用我们整理的数据来发现植物lncrna的功能。总的来说，本研究为lncRNA功能研究提供了一个全面的多维框架，为了解其他植物中lncRNA的功能提供了有价值的参考。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

New Phytologist 生物-植物科学

自引率

5.30%

发文量

728

期刊介绍： New Phytologist is an international electronic journal published 24 times a year. It is owned by the New Phytologist Foundation, a non-profit-making charitable organization dedicated to promoting plant science. The journal publishes excellent, novel, rigorous, and timely research and scholarship in plant science and its applications. The articles cover topics in five sections: Physiology & Development, Environment, Interaction, Evolution, and Transformative Plant Biotechnology. These sections encompass intracellular processes, global environmental change, and encourage cross-disciplinary approaches. The journal recognizes the use of techniques from molecular and cell biology, functional genomics, modeling, and system-based approaches in plant science. Abstracting and Indexing Information for New Phytologist includes Academic Search, AgBiotech News & Information, Agroforestry Abstracts, Biochemistry & Biophysics Citation Index, Botanical Pesticides, CAB Abstracts®, Environment Index, Global Health, and Plant Breeding Abstracts, and others.