Application of Oxford Nanopore Technology to Plant Virus Detection
The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-07-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/13/8/1424 |
| _version_ | 1797521895719960576 |
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| author | Lia W. Liefting David W. Waite Jeremy R. Thompson |
| author_facet | Lia W. Liefting David W. Waite Jeremy R. Thompson |
| author_sort | Lia W. Liefting |
| collection | DOAJ |
| description | The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right. |
| first_indexed | 2024-03-10T08:18:58Z |
| format | Article |
| id | doaj.art-cfdcd1bc314343e7880f0e1388b0b306 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T08:18:58Z |
| publishDate | 2021-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-cfdcd1bc314343e7880f0e1388b0b3062023-11-22T10:09:00ZengMDPI AGViruses1999-49152021-07-01138142410.3390/v13081424Application of Oxford Nanopore Technology to Plant Virus DetectionLia W. Liefting0David W. Waite1Jeremy R. Thompson2Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New ZealandPlant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New ZealandPlant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New ZealandThe adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.https://www.mdpi.com/1999-4915/13/8/1424biosecurityONTMinIONdiagnosticsplant viruseshigh-throughput sequencing |
| spellingShingle | Lia W. Liefting David W. Waite Jeremy R. Thompson Application of Oxford Nanopore Technology to Plant Virus Detection Viruses biosecurity ONT MinION diagnostics plant viruses high-throughput sequencing |
| title | Application of Oxford Nanopore Technology to Plant Virus Detection |
| title_full | Application of Oxford Nanopore Technology to Plant Virus Detection |
| title_fullStr | Application of Oxford Nanopore Technology to Plant Virus Detection |
| title_full_unstemmed | Application of Oxford Nanopore Technology to Plant Virus Detection |
| title_short | Application of Oxford Nanopore Technology to Plant Virus Detection |
| title_sort | application of oxford nanopore technology to plant virus detection |
| topic | biosecurity ONT MinION diagnostics plant viruses high-throughput sequencing |
| url | https://www.mdpi.com/1999-4915/13/8/1424 |
| work_keys_str_mv | AT liawliefting applicationofoxfordnanoporetechnologytoplantvirusdetection AT davidwwaite applicationofoxfordnanoporetechnologytoplantvirusdetection AT jeremyrthompson applicationofoxfordnanoporetechnologytoplantvirusdetection |