Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses

Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to sim...

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Bibliographic Details
Published in:Viruses 2021-03, Vol.13 (4), p.583
Main Authors: Maina, Solomon, Zheng, Linda, Rodoni, Brendan C
Format: Article
Language:English
Subjects:
Australia
crops
diagnostics
Disease management
Gel electrophoresis
Gene mapping
genome
Genome, Viral
Genomes
Germplasm
High-Throughput Nucleotide Sequencing - methods
high-throughput sequencing
Metagenomics
Next-generation sequencing
Pisum sativum - virology
Plant Diseases - virology
plant virus
Plant viruses
Plant Viruses - classification
Plant Viruses - genetics
Potyvirus - genetics
Viruses
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Summary:Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; (PEBV), (CMV), (BYMV) and (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
ISSN:1999-4915
1999-4915
DOI:10.3390/v13040583