Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens

Piombo, Edoardo; Abdelfattah, Ahmed; Droby, Samir; Wisniewski, Michael; Spadaro, D.; Schena, Leonardo

doi:10.3390/microorganisms9010188

Cited by 68 publications

(54 citation statements)

References 148 publications

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“…The new method involves DNA barcoding, which is widely used for species identification and subspecies typing in different fields, including disease monitoring [19]. We amplified a 900-bp portion of the XF genome encompassing part of the HL gene, which is recommended by EPPO international guidelines for the detection of XF and the identification of subspecies [39].…”

Section: Discussionmentioning

confidence: 99%

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Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing

et al. 2022

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Rapid and sensitive assays for the identification of plant pathogens are necessary for the effective management of crop diseases. The main limitation of current diagnostic testing is the inability to combine broad and sensitive pathogen detection with the identification of key strains, pathovars, and subspecies. Such discrimination is necessary for quarantine pathogens, whose management is strictly dependent on genotype identification. To address these needs, we have established and evaluated a novel all-in-one diagnostic assay based on nanopore sequencing for the detection and simultaneous characterization of quarantine pathogens, using Xylella fastidiosa as a case study. The assay proved to be at least as sensitive as standard diagnostic tests and the quantitative results agreed closely with qPCR-based analysis. The same sequencing results also allowed discrimination between subspecies when present either individually or in combination. Pathogen detection and typing were achieved within 13 min of sequencing owing to the use of an internal control that allowed to stop sequencing when sufficient data had accumulated. These advantages, combined with the use of portable equipment, will facilitate the development of next-generation diagnostic assays for the efficient monitoring of other plant pathogens.

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Section: Discussionmentioning

confidence: 99%

“…), oomycetes (Phytophthora spp. ), bacteria ("Candidatus Liberibacter asiaticus"), and viruses (Carrot yellow leaf virus) [19]. Illumina sequencing was recently used to detect and identify particular subspecies of XF; although this method proved efficient, it involves the use of dedicated laboratory facilities and trained personnel [20].…”

Section: Introductionmentioning

confidence: 99%

Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing

et al. 2022

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“…By considering the significance of microbes at various pathways in agricultural production, processing and storage, now scientists are advanced to implement high-throughput sequencing (HTS) for fungal and bacterial diagnosis at various stages. Hence, metagenomics approaches are underway for the detection and surveillance of emerging and recurrent plant pathogens that poses a critical threat on agriculture and its constituent produces (Piombo et al, 2021).…”

Section: Importance Of Microbial Contaminantsmentioning

confidence: 99%

Microbial Contaminants and Their Control Methods: A Review with Reference to Potato Tissue Culture

2021

JNSR

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No cell or tissue culture problem is as universal as that of culture loss due to contamination, so that microbial hazards cause drastic economic losses in the plant tissue culture industries. A wide range of microorganisms (filamentous fungi, yeasts, bacteria, virus and viroid) and micro-arthropods (mites and thrips) have been identified as contaminants in plant tissue culture. With this paramount importance of in-vitro culture contaminants, various research work has been conducted from different corners of the world. This review paper compiles such important information to share experiences within a single amassed document. Different research and review articles, proceedings, protocol notes, scientific notes, conference papers, case reports as well as case studies, research communications and technical reports are included in this paper. Hence, this article aimed to review and provide insights about microbial contaminants and their management techniques and thereby to document the possible attempts made by different scholars to mitigate microbial contamination under plant tissue culture. Moreover, the paper skim through the current advancements made on culture loss due to microbes, their control methods and hostile effects on regeneration capability of culture plants.

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“…In the case of boxwood, Cps , Che , and any other emerging bacterial, fungal, or oomycete boxwood pathogen could be identified. Metagenomics approaches utilizing NGS have been used in clinical research and are gradually being adopted in diagnosing plant diseases as well 13 , 14 . To achieve a rapid diagnosis, the MinION nanopore sequencer, a single‐molecule long-read sequencing platform developed by Oxford Nanopore Technologies Inc. (ONT) is particularly promising.…”

Section: Introductionmentioning

confidence: 99%

Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata

Yang

Johnson

Hansen

et al. 2022

Sci Rep

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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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Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens

Cited by 68 publications

References 148 publications

Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing

Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing

Microbial Contaminants and Their Control Methods: A Review with Reference to Potato Tissue Culture

Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata

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