Direct RNA sequencing in plants:Practical applications and future perspectives  

作　　者：Xi-Tong Zhu Pablo Sanz-Jimenez Xiao-Tong Ning Muhammad Tahir ul Qamar Ling-Ling Chen 

机构地区：[1]State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources,College of Life Science and Technology,Guangxi University,Nanning 530004,China [2]National Key Laboratory of Crop Genetic Improvement,College of Informatics,Huazhong Agricultural University,Wuhan 430070,China [3]Integrative Omics and Molecular Modeling Laboratory,Department of Bioinformatics and Biotechnology,Government College University Faisalabad(GCUF),Faisalabad 38000,Pakistan [4]These authors contributed equally to this article

出　　处：《Plant Communications》2024年第11期54-71,共18页植物通讯（英文）

基　　金：Guangxi Natural Science Foundation(2024GXNSFGA010003);National Natural Science Foundation of China(32270712 and 31871269);Guangxi Science and Technology Major Program(AA23062085).

摘　　要：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.

关 键 词：direct RNA sequencing novel isoforms fusion transcripts poly(A)tail RNA modifications 

分 类 号：Q943.2[生物学—植物学]