Direct RNA sequencing in plants: Practical applications and future perspectives.

IF 9.4 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Plant Communications Pub Date : 2024-11-11 Epub Date: 2024-08-18 DOI:10.1016/j.xplc.2024.101064
Xi-Tong Zhu, Pablo Sanz-Jimenez, Xiao-Tong Ning, Muhammad Tahir Ul Qamar, Ling-Ling Chen
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引用次数: 0

Abstract

The transcriptome serves as a bridge that links genomic variation to phenotypic diversity. A vast number of studies using next-generation RNA sequencing (RNA-seq) over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions, providing numerous insights into the dynamic changes, evolutionary traces, and elaborate regulation of the plant transcriptome. With substantial improvement in accuracy and throughput, direct RNA sequencing (DRS) has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts, overcoming many limitations such as read length and PCR bias that are inherent to short-read RNA-seq. Here, we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach, covering many aspects of RNA metabolism, including novel isoforms, poly(A) tails, and RNA modification, and we propose a comprehensive workflow for processing of plant DRS data. Many challenges to the application of DRS in plants, such as the need for machine learning tools tailored to plant transcriptomes, remain to be overcome, and together we outline future biological questions that can be addressed by DRS, such as allele-specific RNA modification. This technology provides convenient support on which the connection of distinct RNA features is tightly built, sustainably refining our understanding of the biological functions of the plant transcriptome.

植物中的直接 RNA 测序:实际应用与未来展望。
转录组是连接基因组变异和表型多样性的桥梁。近二十年来,大量使用新一代 RNA 测序(RNA-seq)的研究强调了植物转录组在响应发育和环境条件中的重要作用,从而对植物转录组的动态变化、进化轨迹和精细调控有了更多的了解。随着精确度和通量的大幅提高,直接 RNA 测序(DRS)已成为精确检测原生和全长转录本的一种新的强大测序平台,它克服了短读程 RNA-seq 固有的读长和 PCR 偏差等诸多限制。在此,我们从 RNA 代谢的多个方面,包括新型同工酶、poly(A) 尾和 RNA 修饰等,回顾了以 DRS 为主要技术手段剖析植物转录组复杂性和多样性的最新进展,并提出了一套完整的植物 DRS 数据处理工作流程。关于 DRS 在植物中的应用,还有许多挑战有待解决,如针对植物转录组的机器学习工具,我们一起展望了 DRS 有可能回答的未来生物学问题,如等位基因特异性 RNA 修饰。这项技术提供了便捷的支持,可在此基础上紧密建立不同 RNA 特征之间的联系,从而不断完善我们对植物转录组生物学功能的理解。
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
Plant Communications
Plant Communications Agricultural and Biological Sciences-Plant Science
CiteScore
15.70
自引率
5.70%
发文量
105
审稿时长
6 weeks
期刊介绍: Plant Communications is an open access publishing platform that supports the global plant science community. It publishes original research, review articles, technical advances, and research resources in various areas of plant sciences. The scope of topics includes evolution, ecology, physiology, biochemistry, development, reproduction, metabolism, molecular and cellular biology, genetics, genomics, environmental interactions, biotechnology, breeding of higher and lower plants, and their interactions with other organisms. The goal of Plant Communications is to provide a high-quality platform for the dissemination of plant science research.
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