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How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?

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Abstract

Key message

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.

Abstract

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.

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Acknowledgements

This research was funded by the Japan Society for the Promotion of Science (JSPS) under the Fund of Grant-in-Aid (project number: 20F20392) for JSPS Fellow Islam Hamim (fellowship ID. F20392).

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Authors and Affiliations

  1. Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan

    Islam Hamim & Ken Komatsu

  2. International Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan

    Islam Hamim

  3. Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh

    Islam Hamim

  4. Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan

    Ken-Taro Sekine

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  1. Islam Hamim
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  2. Ken-Taro Sekine
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  3. Ken Komatsu
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Conceptualization: IH; Literature search: IH, KK; Writing—original draft preparation: IH Writing—review and editing: IH, KK, KS; Funding acquisition: IH, KK; Supervision: KK.

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Correspondence to Ken Komatsu.

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Hamim, I., Sekine, KT. & Komatsu, K. How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?. Plant Mol Biol 110, 469–484 (2022). https://doi.org/10.1007/s11103-022-01305-5

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