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

Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

(2020) Jorge Lalucat et al.   Genes

Development of a sensitive TaqMan® qPCR assay for detection and quantification of Venturia inaequalis in apple leaves and fruit and in air samples

(2020) Simona Prencipe et al.   PLANT DISEASE

New Molecular Tool for a Quick and Easy Detection of Apple Scab in the Field

(2020) Sara Franco Ortega et al.   Agronomy-Basel

Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple

(2020) Ahmed Abdelfattah et al.   Microorganisms

Plant pathogenic fungi are harbored as endophytes in Rhododendron spp. native to the Eastern U.S.A.

(2020) Timothy L. Widmer et al.   Fungal Ecology

Monitoring and Surveillance of Aerial Mycobiota of Rice Paddy through DNA Metabarcoding and qPCR

(2020) Sara Franco Ortega et al.   Journal of Fungi

Metabarcoding targeting the EF1 alpha region to assess Fusarium diversity on cereals

(2019) Anne-Laure Boutigny et al.   PLoS One

Use of Next Generation Sequencing to study two cowpox virus outbreaks

(2019) Markus H. Antwerpen et al.   PeerJ

Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing

(2019) Jean Legeay et al.   JOURNAL OF PLANT PATHOLOGY

Rapid detection of Monilinia fructicola and Monilinia laxa on peaches and nectarines using loop-mediated isothermal amplification

(2019) SARA FRANCO ORTEGA et al.   PLANT DISEASE

Are traded forest tree seeds a potential source of nonnative pests?

(2019) Iva Franić et al.   ECOLOGICAL APPLICATIONS

Managing climate change risks in global supply chains: a review and research agenda

(2019) Abhijeet Ghadge et al.   INTERNATIONAL JOURNAL OF PRODUCTION RESEARCH

Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk

(2019) Tulsi K. Joishy et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Nanotechnology in Plant Science: To Make a Long Story Short

(2019) Ilaria Sanzari et al.   Frontiers in Bioengineering and Biotechnology

Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases

(2019) Peter Gerner-Smidt et al.   Frontiers in Public Health

Revealing Cues for Fungal Interplay in the Plant–Air Interface in Vineyards

(2019) Ahmed Abdelfattah et al.   Frontiers in Plant Science

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

(2019) Charlie Pauvert et al.   Fungal Ecology

Diversity of Phytophthora Species Associated with Quercus ilex L. in Three Spanish Regions Evaluated by NGS

(2019) Beatriz Mora-Sala et al.   Forests

Whole Genome Shotgun Sequencing Detects Greater Lichen Fungal Diversity Than Amplicon-Based Methods in Environmental Samples

(2019) Kyle Garrett Keepers et al.   Frontiers in Ecology and Evolution

Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies

(2018) Ahmed Abdelfattah et al.   BIOLOGICAL CONTROL

Different Lactobacillus populations dominate in “ Chorizo de León ” manufacturing performed in different production plants

(2018) Narciso M. Quijada et al.   FOOD MICROBIOLOGY

Several species of Penicillium isolated from chestnut flour processing are pathogenic on fresh chestnuts and produce mycotoxins

(2018) Simona Prencipe et al.   FOOD MICROBIOLOGY

Characterization of Aspergillus section Flavi isolated from fresh chestnuts and along the chestnut flour process

(2018) Simona Prencipe et al.   FOOD MICROBIOLOGY

Penicillium gravinicasei , a new species isolated from cave cheese in Apulia, Italy

(2018) Pamela Anelli et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

(2018) Teresita M. Porter et al.   MOLECULAR ECOLOGY

A fungal mock community control for amplicon sequencing experiments

(2018) Matthew G. Bakker   Molecular Ecology Resources

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Screening for exotic forest pathogens to increase survey capacity using metagenomics

(2018) Emilie D. Tremblay et al.   PHYTOPATHOLOGY

Development of Loop-Mediated Isothermal Amplification Assays for the Detection of Seedborne Fungal Pathogens Fusarium fujikuroi and Magnaporthe oryzae in Rice Seed

(2018) Sara Franco Ortega et al.   PLANT DISEASE

Rapid detection of Fusarium oxysporum f. sp. lactucae on soil, lettuce seeds and plants using loop-mediated isothermal amplification

(2018) S. Franco Ortega et al.   PLANT PATHOLOGY

The fruit and vegetable import pathway for potential invasive pest arrivals

(2018) Erik Lichtenberg et al.   PLoS One

Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection

(2018) Vrantika Chaudhary et al.   JOURNAL OF NANOBIOTECHNOLOGY

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities

(2018) Jaime Aguayo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

(2018) Nicholas D Sanderson et al.   BMC GENOMICS

The impact of high throughput sequencing on plant health diagnostics

(2018) Ian P. Adams et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Slippage of degenerate primers can cause variation in amplicon length

(2018) Vasco Elbrecht et al.   Scientific Reports

High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

(2018) Leho Tedersoo et al.   Molecular Ecology Resources

Mycobiome diversity: high-throughput sequencing and identification of fungi

(2018) R. Henrik Nilsson et al.   NATURE REVIEWS MICROBIOLOGY

Xylella fastidiosa in Olive in Apulia: Where We Stand

(2018) M. Saponari et al.   PHYTOPATHOLOGY

Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases

(2018) Maxime Gaudin et al.   Frontiers in Microbiology

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

(2017) Yusuke Okazaki et al.   ISME Journal

UniEuk : Time to Speak a Common Language in Protistology!

(2017) Cédric Berney et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

A world of opportunities with nanopore sequencing

(2017) Richard M Leggett et al.   JOURNAL OF EXPERIMENTAL BOTANY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Development and Validation of a TaqMan Real-Time PCR Assay for the Specific Detection and Quantification of Fusarium fujikuroi in Rice Plants and Seeds

(2017) Greice Amaral Carneiro et al.   PHYTOPATHOLOGY

Phylogeny and Haplotype Analysis of Fungi Within the Fusarium incarnatum-equiseti Species Complex

(2017) H. Ramdial et al.   PHYTOPATHOLOGY

On site DNA barcoding by nanopore sequencing

(2017) Michele Menegon et al.   PLoS One

Specific and Sensitive Isothermal Electrochemical Biosensor for Plant Pathogen DNA Detection with Colloidal Gold Nanoparticles as Probes

(2017) Han Yih Lau et al.   Scientific Reports

Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water

(2017) Ru Li et al.   Scientific Reports

Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes

(2017) Michelle A. Berry et al.   Frontiers in Microbiology

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Degenerate primers as biomarker for gene-targeted metagenomics of the catechol 1, 2-dioxygenase-encoding gene in microbial populations of petroleum-contaminated environments

(2016) Fatemeh Nafian et al.   ANNALS OF MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

High-resolution community profiling of arbuscular mycorrhizal fungi

(2016) Klaus Schlaeppi et al.   NEW PHYTOLOGIST

Metabarcoding Analysis of Phytophthora Diversity Using Genus-Specific Primers and 454 Pyrosequencing

(2016) Maria I. Prigigallo et al.   PHYTOPATHOLOGY

Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

(2016) Teresita M. Porter et al.   PLoS One

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA

(2016) Thomas Sauvage et al.   BMC ECOLOGY

Innovations in air sampling to detect plant pathogens

(2015) J.S. West et al.   ANNALS OF APPLIED BIOLOGY

Genus-Specific Primers for Study of Fusarium Communities in Field Samples

(2015) Ida Karlsson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of Putative Coffee Rust Mycoparasites via Single-Molecule DNA Sequencing of Infected Pustules

(2015) Timothy Y. James et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Next generation sequencing and its applications in forensic genetics

(2015) Claus Børsting et al.   Forensic Science International-Genetics

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

(2015) J.B. Stielow et al.   PERSOONIA

Molecular analysis ofPhytophthoradiversity in nursery-grown ornamental and fruit plants

(2015) M. I. Prigigallo et al.   PLANT PATHOLOGY

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

(2015) Amelia Hubbard et al.   GENOME BIOLOGY

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

(2015) Leho Tedersoo et al.   MycoKeys

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain

(2015) Santiago Català et al.   PLoS One

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea)

(2015) Ahmed Abdelfattah et al.   PLoS One

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Plant–fungal interactions: What triggers the fungi to switch among lifestyles?

(2014) Mahendra Rai et al.   CRITICAL REVIEWS IN MICROBIOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Molecular Analysis of Colletotrichum Species in the Carposphere and Phyllosphere of Olive

(2014) Saveria Mosca et al.   PLoS One

Carrot yellow leaf virus Is Associated with Carrot Internal Necrosis

(2014) Ian P. Adams et al.   PLoS One

Phylogeny, identification and nomenclature of the genus Aspergillus

(2014) R.A. Samson et al.   STUDIES IN MYCOLOGY

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

The aerobiology of Fusarium graminearum

(2013) Melissa D. Keller et al.   AEROBIOLOGIA

Biology, Epidemiology, and Control ofHeterobasidionSpecies Worldwide

(2013) Matteo Garbelotto et al.   Annual Review of Phytopathology

Fundamentals of Pyrosequencing

(2013) Colleen T. Harrington et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities

(2013) Alissa S. Hanshew et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Use of Quantitative PCR Detection Methods to Study Biocontrol Agents and Phytopathogenic Fungi and Oomycetes in Environmental Samples

(2013) Simona M. Sanzani et al.   JOURNAL OF PHYTOPATHOLOGY

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

(2013) Natacha Bodenhausen et al.   PLoS One

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crop losses due to diseases and their implications for global food production losses and food security

(2012) Serge Savary et al.   Food Security

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

A molecular method to assess Phytophthora diversity in environmental samples

(2011) Silvia Scibetta et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other's development

(2011) M. A. Friedl et al.   MICROBIOLOGY-SGM

Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing

(2011) Lei Chen et al.   PLANTA

Global food demand and the sustainable intensification of agriculture

(2011) D. Tilman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny of Penicillium and the segregation of Trichocomaceae into three families

(2011) J. Houbraken et al.   STUDIES IN MYCOLOGY

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems

(2010) Minou Nowrousian   EUKARYOTIC CELL

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

The future of the global food system

(2010) H. C. J. Godfray et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular identification of Fusarium spp. associated with bakanae disease of rice in Italy and assessment of their pathogenicity

(2010) M. T. Amatulli et al.   PLANT PATHOLOGY

Phytophthora lateralis discovered in an old growth Chamaecyparis forest in Taiwan

(2010) C. M. Brasier et al.   PLANT PATHOLOGY

Food Security: The Challenge of Feeding 9 Billion People

(2010) H. C. J. Godfray et al.   SCIENCE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete Genome Sequence of Citrus Huanglongbing Bacterium, ‘CandidatusLiberibacter asiaticus’ Obtained Through Metagenomics

(2009) Yongping Duan et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Heterobasidion annosumandH. parviporumin the Southern Rocky Mountains and Adjoining States

(2009) James J. Worrall et al.   PLANT DISEASE

Constatação de Xylella fastidiosa em pecíolos e hipocotilos de cafeeiro com sintomas de mancha manteigosa

(2008) Severina Rodrigues de Oliveira Lins et al.   CIENCIA E AGROTECNOLOGIA