ArticleScientific reports2022
Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
- Research progress on nucleic acid amplification-based detection technologies for phytopathogenic fungi.Applied microbiology and biotechnology · 2026Review
- MinION Nanopore-Enabled Identification and Genomic Characterization of Pseudomonas syringae Complex Infecting Blueberry Using Symptomatic Plant Samples and Pathogen Pure Culture.Current protocols · 2026Article
- Molecular Identification and RNA-Based Management of Fungal Plant Pathogens: From PCR to CRISPR/Cas9.International journal of molecular sciences · 2026Review
- Machine-learning-based analysis of host-depletedBioinformatics advances · 2026Article
- PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.GigaScience · 2025Article
- Genomics in plant pathogen identification and control.Frontiers in plant science · 2025Review
- Optimizing next-generation sequencing efficiency in clinical settings: analysis of read length impact on cost and performance.BMC genomics · 2024Article
- Seeing in the dark: a metagenomic approach can illuminate the drivers of plant disease.Frontiers in plant science · 2024Article
- Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing.PloS one · 2024Article
- Reference-Free Plant Disease Detection Using Machine Learning and Long-Read Metagenomic Sequencing.Applied and environmental microbiology · 2023Article
- Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests.Plants (Basel, Switzerland) · 2023Article
- Current and emerging trends in techniques for plant pathogen detection.Frontiers in plant science · 2023Review
- Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnostic of Fungal Pathogens in Plants.Journal of fungi (Basel, Switzerland) · 2022Review
- New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?Journal of fungi (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pathogen detection and identification are key elements in outbreak control of human, animal, and plant diseases. Since many fungal plant pathogens cause similar symptoms, are difficult to distinguish morphologically, and grow slowly in culture, culture-independent, sequence-based diagnostic methods are desirable. Whole genome metagenomic sequencing has emerged as a promising technique because it can potentially detect any pathogen without culturing and without the need for pathogen-specific probes. However, efficient DNA extraction protocols, computational tools, and sequence databases are required. Here we applied metagenomic sequencing with the Oxford Nanopore Technologies MinION to the detection of the fungus Calonectria pseudonaviculata, the causal agent of boxwood (Buxus spp.) blight disease. Two DNA extraction protocols, several DNA purification kits, and various computational tools were tested. All DNA extraction methods and purification kits provided sufficient quantity and quality of DNA. Several bioinformatics tools for taxonomic identification were found suitable to assign sequencing reads to the pathogen with an extremely low false positive rate. Over 9% of total reads were identified as C. pseudonaviculata in a severely diseased sample and identification at strain-level resolution was approached as the number of sequencing reads was increased. We discuss how metagenomic sequencing could be implemented in routine plant disease diagnostics.
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