Medhi Upasana, Chaliha Chayanika, Singh Archana, Nath Bikash K, Kalita Eeshan
Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences-CAU Imphal, Umiam, Meghalaya, 793104, India.
Gene. 2025 Mar 10;940:149187. doi: 10.1016/j.gene.2024.149187. Epub 2024 Dec 24.
In recent years, third-generation sequencing (TGS) technologies have transformed genomics and transcriptomics research, providing novel opportunities for significant discoveries. The long-read sequencing platforms, with their unique advantages over next-generation sequencing (NGS), including a definitive protocol, reduced operational time, and real-time sequencing, possess the potential to transform plant genomics. TGS optimizes and enhances the efficiency of data analysis by removing the necessity for time-consuming assembly tools. The current review examines the development and application of bioinformatics tools for data analysis and annotation, driven by the rapid advancement of TGS platforms like Oxford Nanopore Technologies and Pacific Biosciences. Transcriptome analysis utilizing TGS has been extensively employed to elucidate complex plant transcriptomes and genomes, particularly those characterized by high frequencies of duplicated genomes and repetitive sequences. As a result, current methodologies that allow for generating transcriptomes and comprehensive whole-genome sequences of complex plant genomes employing tailored hybrid sequencing techniques that integrate NGS and TGS technologies have been emphasized herein. This paper, thus, articulates a vision for a future in which TGS effectively addresses the challenges faced in plant research, offering a comprehensive understanding of its advantages, applications, limitations, and promising prospects.
近年来，第三代测序（TGS）技术变革了基因组学和转录组学研究，为重大发现提供了新机遇。长读长测序平台相对于下一代测序（NGS）具有独特优势，包括确定的方案、缩短的操作时间和实时测序，具备变革植物基因组学的潜力。TGS通过消除对耗时组装工具的需求，优化并提高了数据分析效率。本综述探讨了由牛津纳米孔技术公司和太平洋生物科学公司等TGS平台的快速发展所推动的用于数据分析和注释的生物信息学工具的开发与应用。利用TGS进行的转录组分析已被广泛用于阐明复杂的植物转录组和基因组，特别是那些具有高频率重复基因组和重复序列特征的转录组和基因组。因此，本文强调了当前利用整合NGS和TGS技术的定制杂交测序技术生成复杂植物基因组转录组和全面全基因组序列的方法。本文阐述了一个未来愿景，即TGS有效应对植物研究中面临的挑战，全面介绍其优势、应用、局限性和广阔前景。
