Diagnosis of plant diseases using the Nanopore sequencing platform
| Autor: | Victor Gaba, O. Dror, Aviv Dombrovsky, M. Reuven, Neta Luria, G. Nissan, A. Beerman, Oded Lachman, Shulamit Manulis-Sasson, Laura Chalupowicz |
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| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
0301 basic medicine Whole genome sequencing Plant Science Computational biology Horticulture Biology biology.organism_classification 01 natural sciences Genome DNA sequencing law.invention 03 medical and health sciences Nanopore 030104 developmental biology law Phytoplasma Genetics Nucleic acid Nanopore sequencing Agronomy and Crop Science Polymerase chain reaction 010606 plant biology & botany |
| Zdroj: | Plant Pathology. 68:229-238 |
| ISSN: | 0032-0862 |
| DOI: | 10.1111/ppa.12957 |
| Popis: | Reliable detection and identification of plant pathogens are essential for disease control strategies. Diagnostic methods commonly used to detect plant pathogens have limitations such as requirement of prior knowledge of the genome sequence, low sensitivity and a restricted ability to detect several pathogens simultaneously. The development of advanced DNA sequencing technologies has enabled determination of total nucleic acid content in biological samples. The possibility of using the single‐molecule sequencing platform of Oxford Nanopore as a general method for diagnosis of plant diseases was examined. It was tested by sequencing DNA or RNA isolated from tissues with symptoms from plants of several families inoculated with known pathogens (e.g. bacteria, viruses, fungi, phytoplasma). Additionally, samples of groups of 200 seeds containing one infected seed of each of two or three pathogens, as well as samples with symptoms but unidentified pathogens were tested. Sequencing results were analysed with Nanopore data analysis tools. In all the inoculated plants, pathogens were identified in real time within 1–2 h of running the Nanopore sequencer and were classified to the species or genus level. DNA sequencing or direct RNA sequencing of samples with unidentified disease agents were validated by conventional diagnostic procedures (e.g. PCR, ELISA, Koch test), which supported the results obtained by Nanopore sequencing. The advantages of this technology include: long read lengths, fast run times, portability, low cost and the possibility of use in every laboratory. This study indicates that adoption of the Nanopore platform will be greatly advantageous for routine laboratory diagnosis. |
| Databáze: | OpenAIRE |
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