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The use of third generation sequencing tool for detection and identification of plant pathogens

Laura Chalupowicz: ARO, The Volcani Center

<div>Crop infections by plant pathogens are a persistent economic threat worldwide. Reliable identification of the disease causal agent is essential for disease management strategies. The diagnostic methods commonly used to detect plant pathogens have some limitations such as low sensitivity, requirement of prior knowledge of the genome sequence, and are limited in detection of several pathogens simultaneously. In recent years, the development of advanced DNA sequencing technologies has enabled determination of total nucleic acid content in biological samples and thus provides a powerful diagnostic tool. In this study, we used the third generation sequencing platform of Oxford Nanopore, which enables sequencing of long reads when a single-stranded DNA molecule passes through a biological pore of the MinION sequencer. Extraction methods to obtain high molecular weight total DNA and sequence runs for 6-16 h were sufficient to yield enough data for real time species identification. The applicability of this technology for detection of bacterial and fungal pathogens in tomato seeds has been tested. In addition, DNA extracted from samples of symptomatic plants of unknown source were sequenced and the results provide indications for possible disease causal agents. This technology has the potential use for laboratory and field detection of plant pathogens including those that are unculturable or unknown.</div>