ArticleFrontiers in plant science2022
High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing.
Article in Frontiers in plant science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 20 citations in OpenAlex.
- Article
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- Comprehensive virome analysis of potato crops in Bangladesh reveals diverse viral communities and the first report of potato virus V.Virology journal · 2026Article
- Comprehensive Virome Analysis of Commercial Lilies in South Korea by RT-PCR, High-Throughput Sequencing, and Phylogenetic Analyses.International journal of molecular sciences · 2025Article
- Recent advances in characterization and diagnosis of stone fruit tree viruses.Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Review
- Nanopore Workflow for Grapevine Viroid Surveillance in Kazakhstan: Bypassing rRNA Depletion Through Non-Canonical Priming.Pathogens (Basel, Switzerland) · 2025Article
- A comparative template-switching cDNA approach for HTS-based multiplex detection of three viruses and one viroid commonly found in apple trees.Scientific reports · 2025Article
- New insights into viral threats in soybean (Frontiers in microbiology · 2025Article
- Investigating the Role of Viruses in the Rapid Decline of Young Apple Trees in High-Density Orchards in New York.Plants (Basel, Switzerland) · 2024Article
- High-Throughput Sequencing Methods for the Detection of Two Strawberry Viruses in Post-Entry Quarantine.Viruses · 2024Article
- Development of a CRISPR/SHERLOCK-Based Method for Rapid and Sensitive Detection of Selected Pospiviroids.Viruses · 2024Article
- Article
- PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data.BMC bioinformatics · 2023Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A comprehensive diagnostic method of known plant viruses and viroids is necessary to provide an accurate phytosanitary status of fruit trees. However, most widely used detection methods have a small limit on either the number of targeted viruses/viroids or the number of samples to be evaluated at a time, hampering the ability to rapidly scale up the test capacity. Here we report that by combining the power of high multiplexing PCR (499 primer pairs) of small amplicons (120-135bp), targeting 27 viruses and 7 viroids of fruit trees, followed by a single high-throughput sequencing (HTS) run, we accurately diagnosed the viruses and viroids on as many as 123 pome and stone fruit tree samples. We compared the accuracy, sensitivity, and reproducibility of this approach and contrast it with other detection methods including HTS of total RNA (RNA-Seq) and individual RT-qPCR for every fruit tree virus or viroid under the study. We argue that this robust and high-throughput cost-effective diagnostic tool will enhance the viral/viroid knowledge of fruit trees while increasing the capacity for large scale diagnostics. This approach can also be adopted for the detection of multiple viruses and viroids in other crops.
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