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References from Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Local targets link to admitted publications; unresolved targets remain external evidence.
The impact of high throughput sequencing on plant health diagnostics
10.1007/s10658-018-1570-0 · 2018 · External reference
Carrot yellow leaf virus Is Associated with Carrot Internal Necrosis
10.1371/journal.pone.0109125 · 2014 · External reference
Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities
10.1128/aem.02637-17 · 2018 · External reference
Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses
10.1007/s00705-010-0869-8 · 2011 · External reference
College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests
10.5858/arpa.2014-0250-cp · 2015 · External reference
Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment
10.1016/j.watres.2020.115628 · 2020 · External reference
Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data
10.1099/jgv.0.001210 · 2019 · External reference
A fungal mock community control for amplicon sequencing experiments
10.1111/1755-0998.12760 · 2018 · External reference
Detection of Diplodia corticola spores in Ontario and Québec based on High Throughput Sequencing (HTS) methods
10.1080/07060661.2018.1498394 · 2018 · External reference
Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids
10.1186/s12985-021-01523-1 · 2021 · External reference
Development and Evaluation of a Triplex TaqMan Assay and Next-Generation Sequence Analysis for Improved Detection of Xylella in Plant Material
10.1094/pdis-08-18-1433-re · 2019 · External reference
Screening for sugarcane yellow leaf virus in sorghum in Florida revealed its occurrence in mixed infections with sugarcane mosaic virus and a new marafivirus
10.1016/j.cropro.2020.105373 · 2021 · External reference
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets
10.1128/jcm.00466-19 · 2019 · External reference
A DNA barcoding approach to identify plant species in multiflower honey
10.1016/j.foodchem.2014.08.060 · 2015 · External reference
Validation of high throughput sequencing and microbial forensics applications
10.1186/2041-2223-5-9 · 2014 · External reference
Seasonal Variation of Ralstonia solanacearum Biovar 2 Populations in a Spanish River: Recovery of Stressed Cells at Low Temperatures
10.1128/aem.71.1.140-148.2005 · 2005 · External reference
Comparison of qPCR and Metabarcoding Methods as Tools for the Detection of Airborne Inoculum of Forest Fungal Pathogens
10.1094/phyto-02-20-0034-r · 2021 · External reference
To tell or not to tell? A systematic review of ethical reflections on incidental findings arising in genetics contexts
10.1038/ejhg.2012.130 · 2013 · External reference
From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study
10.1016/bs.aivir.2018.02.003 · 2018 · External reference
Pathogenicity and virulence gene content of Xanthomonas strains infecting Araceae, formerly known as Xanthomonas axonopodis pv. dieffenbachiae
10.1111/ppa.12694 · 2017 · External reference
Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids
10.1016/j.jmoldx.2019.05.002 · 2019 · External reference
Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples
10.1373/clinchem.2016.258806 · 2016 · External reference
Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline
10.1038/ismej.2017.170 · 2018 · External reference
Evaluation of sensitivity and specificity in RNA-Seq-based detection of grapevine viral pathogens
10.1016/j.jviromet.2021.114383 · 2022 · External reference
Validation of COI metabarcoding primers for terrestrial arthropods
10.7717/peerj.7745 · 2019 · External reference
Reconsidering causal association in plant virology
10.1111/ppa.13199 · 2020 · External reference
Using high‐throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae)
10.1111/ppa.12962 · 2019 · External reference
Potato virus Y; the Andean connection
10.1093/ve/vez037 · 2019 · External reference
First report of Southern tomato virus in German tomatoes
10.5197/j.2044-0588.2019.040.001 · 2019 · External reference
Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing
10.1371/journal.pone.0237951 · 2020 · External reference
16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife
10.1128/msystems.00032-16 · 2016 · External reference
Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification
10.1007/s00705-012-1253-7 · 2012 · External reference
Detection of Banana Mild Mosaic Virus in Musa In Vitro Plants: High-Throughput Sequencing Presents Higher Diagnostic Sensitivity Than (IC)-RT-PCR and Identifies a New Betaflexiviridae Species
10.3390/plants11020226 · 2022 · External reference
Pepino mosaic virus isolates and differential symptomatology in tomato
10.1111/j.1365-3059.2008.02018.x · 2009 · External reference
Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis
10.1038/s41467-018-05555-0 · 2018 · External reference
The Belgian next generation sequencing guidelines for haematological and solid tumours
2017 · External reference
Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots: A morphological and metabarcoding approach
10.1371/journal.pone.0230153 · 2020 · External reference
Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses
10.3389/fmicb.2020.592816 · 2020 · External reference
Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels
10.1016/j.jmoldx.2017.01.011 · 2017 · External reference
Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control
10.1016/j.jviromet.2016.07.001 · 2016 · External reference
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
10.1093/bioinformatics/bts611 · 2012 · External reference
Synergisms between microbial pathogens in plant disease complexes: a growing trend
10.3389/fpls.2015.00385 · 2015 · External reference
Facilitating the adoption of high‐throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step‐by‐step description
10.1111/epp.12863 · 2022 · External reference
Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization
10.1093/nar/gkv303 · 2015 · External reference
Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales
10.3389/fmicb.2020.578064 · 2020 · External reference
Sarcococca Blight: Use of Whole-Genome Sequencing for Fungal Plant Disease Diagnosis
10.1094/pdis-10-15-1159-re · 2016 · External reference
Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges
10.3389/fpls.2018.01082 · 2018 · External reference
Impacts of Molecular Diagnostic Technologies on Plant Disease Management
10.1146/annurev.phyto.38.1.207 · 2000 · External reference
Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes
10.1016/j.virusres.2015.11.002 · 2016 · External reference
A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies
10.3389/fmicb.2017.00045 · 2017 · External reference
Virus Detection by High-Throughput Sequencing of Small RNAs: Large-Scale Performance Testing of Sequence Analysis Strategies
10.1094/phyto-02-18-0067-r · 2019 · External reference
Current impact and future directions of high throughput sequencing in plant virus diagnostics
10.1016/j.virusres.2014.03.029 · 2014 · External reference
Descriptive assessment of uncertainties of qualitative real-time PCR for detection of plant pathogens and quality performance monitoring
10.1111/epp.12166 · 2014 · External reference
Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
10.1101/gr.238170.118 · 2019 · External reference
A Grain Rot of Rice in Iran Caused by a Xanthomonas Strain Closely Related to X. sacchari
10.1094/pdis-01-20-0179-sc · 2020 · External reference
An operational risk assessment framework for a plant health diagnostic laboratory
10.1111/epp.12477 · 2018 · External reference
Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing
10.1128/aem.00472-17 · 2017 · External reference
High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities
10.1111/epp.12472 · 2018 · External reference
Root‐lesion nematodes of potato: Current status of diagnostics, pathogenicity and management
10.1111/ppa.13144 · 2020 · External reference
Molecular Tools for Diagnostics
10.1007/978-94-007-0434-3_21 · 2011 · External reference
Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data
10.7717/peerj.4925 · 2018 · External reference
Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches
10.3389/fmicb.2017.01998 · 2017 · External reference
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
10.1093/gigascience/giz092 · 2019 · External reference
PM 7/77 (3) Documentation and reporting on a diagnosis
10.1111/epp.12628 · 2019 · External reference
PM 7/76 (5) Use of EPPO Diagnostic Standards
10.1111/epp.12506 · 2018 · External reference
PM 7/98 (4) Specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity
10.1111/epp.12629 · 2019 · External reference
PM 7/147 (1) Guidelines for the production of biological reference material
10.1111/epp.12781 · 2021 · External reference
ACMG clinical laboratory standards for next-generation sequencing
10.1038/gim.2013.92 · 2013 · External reference
Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain
10.7717/peerj.6931 · 2019 · External reference
Ensuring validation in diagnostic testing is fit for purpose: a view from the plant virology laboratory
10.1111/epp.12445 · 2018 · External reference
Classical and next generation sequencing approaches unravel Bymovirus diversity in barley crops in France
10.1371/journal.pone.0188495 · 2017 · External reference
Validation of high throughput sequencing as virus indexing test for Musa germplasm: performance criteria evaluation and contamination monitoring using an alien control
10.1094/phytofr-03-22-0030-fi · 2022 · External reference
Plants, viruses and the environment: Ecology and mutualism
10.1016/j.virol.2015.03.041 · 2015 · External reference
Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines
10.1016/j.jmoldx.2017.11.003 · 2018 · External reference
Sensitivity of Small RNA-Based Detection of Plant Viruses
10.3389/fmicb.2018.00939 · 2018 · External reference
Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection
10.5858/arpa.2016-0539-ra · 2017 · External reference
Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics
10.3390/v13061130 · 2021 · External reference
10.24072/pcjournal.62 · 2021 · Admitted local publication
Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time
10.1094/pdis-12-21-2800-re · 2022 · External reference
Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods
10.1002/ece3.4809 · 2019 · External reference
Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls
10.1038/s41598-018-27314-3 · 2018 · External reference
Screening for Exotic Forest Pathogens to Increase Survey Capacity Using Metagenomics
10.1094/phyto-02-18-0028-r · 2018 · External reference
VALITEST: Validation of diagnostic tests to support plant health
10.1111/epp.12740 · 2021 · External reference
Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients
10.1016/j.jmoldx.2019.10.007 · 2020 · External reference
Next-generation sequencing for virus detection: covering all the bases
10.1186/s12985-016-0539-x · 2016 · External reference
