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Direct RNA sequencing in plants:Practical applications and future perspectives

Plant Communications 2024年第11期5卷 54-71页

作者： Xi-Tong Zhu Pablo Sanz-Jimenez Xiao-Tong Ning Muhammad Tahir ul Qamar Ling-Ling Chen State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Integrative Omics and Molecular Modeling Laboratory Department of Bioinformatics and BiotechnologyGovernment College University Faisalabad(GCUF)Faisalabad 38000Pakistan These authors contributed equally to this article

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 *** 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 ***,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 *** 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 *** 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.

关键词： direct RNA sequencing novel isoforms fusion transcripts poly(A)tail RNA modifications

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