Hamim Islam, Sekine Ken-Taro, Komatsu Ken
Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan.
International Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan.
Plant Mol Biol. 2022 Dec;110(6):469-484. doi: 10.1007/s11103-022-01305-5. Epub 2022 Aug 13.
Long-read sequencing technologies are revolutionizing the sequencing and analysis of plant and pathogen genomes and transcriptomes, as well as contributing to emerging areas of interest in plant-pathogen interactions, disease management techniques, and the introduction of new plant varieties or cultivars. Long-read sequencing (LRS) technologies are progressively being implemented to study plants and pathogens of agricultural importance, which have substantial economic effects. The variability and complexity of the genome and transcriptome affect plant growth, development and pathogen responses. Overcoming the limitations of second-generation sequencing, LRS technology has significantly increased the length of a single contiguous read from a few hundred to millions of base pairs. Because of the longer read lengths, new analysis methods and tools have been developed for plant and pathogen genomics and transcriptomics. LRS technologies enable faster, more efficient, and high-throughput ultralong reads, allowing direct sequencing of genomes that would be impossible or difficult to investigate using short-read sequencing approaches. These benefits include genome assembly in repetitive areas, creating more comprehensive and exact genome determinations, assembling full-length transcripts, and detecting DNA and RNA alterations. Furthermore, these technologies allow for the identification of transcriptome diversity, significant structural variation analysis, and direct epigenetic mark detection in plant and pathogen genomic regions. LRS in plant pathology is found efficient for identifying and characterization of effectors in plants as well as known and unknown plant pathogens. In this review, we investigate how these technologies are transforming the landscape of determination and characterization of plant and pathogen genomes and transcriptomes efficiently and accurately. Moreover, we highlight potential areas of interest offered by LRS technologies for future study into plant-pathogen interactions, disease control strategies, and the development of new plant varieties or cultivars.
长读长测序技术正在彻底改变植物和病原体基因组及转录组的测序与分析方式，同时也为植物 - 病原体相互作用、病害管理技术以及新植物品种或栽培品种引入等新兴研究领域做出贡献。长读长测序（LRS）技术正逐渐应用于研究具有重大经济影响的重要农业植物和病原体。基因组和转录组的变异性与复杂性会影响植物生长、发育及病原体反应。长读长测序技术克服了第二代测序的局限性，将单个连续读长从几百个碱基对大幅增加到数百万个碱基对。由于读长更长，针对植物和病原体基因组学及转录组学开发了新的分析方法和工具。长读长测序技术能够实现更快、更高效且高通量的超长读长，使得使用短读长测序方法无法或难以研究的基因组能够直接测序。这些优势包括在重复区域进行基因组组装、实现更全面准确的基因组测定、组装全长转录本以及检测DNA和RNA改变。此外，这些技术还能用于鉴定转录组多样性、进行显著结构变异分析以及直接检测植物和病原体基因组区域的表观遗传标记。在植物病理学中，长读长测序被发现对于鉴定和表征植物中的效应子以及已知和未知的植物病原体非常有效。在本综述中，我们探讨了这些技术如何高效且准确地改变植物和病原体基因组及转录组的测定与表征格局。此外，我们还强调了长读长测序技术为未来植物 - 病原体相互作用、病害控制策略以及新植物品种或栽培品种开发研究提供的潜在关注领域。
