Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding

Novel Seimatosporium Species from Grapevine in Northern California and Their Interactions with Fungal Pathogens Involved in the Trunk-Disease Complex

(2018) Daniel P. Lawrence et al.   PLANT DISEASE

Managing Grapevine Trunk Diseases With Respect to Etiology and Epidemiology: Current Strategies and Future Prospects

(2018) David Gramaje et al.   PLANT DISEASE

Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

(2018) Mélanie Massonnet et al.   Frontiers in Microbiology

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex

(2017) Abraham Morales-Cruz et al.   MOLECULAR PLANT PATHOLOGY

A Method to Detect and Quantify Eutypa lata and Diplodia seriata-Complex DNA in Grapevine Pruning Wounds

(2017) Jérôme Pouzoulet et al.   PLANT DISEASE

Various fungal communities colonise the functional wood tissues of old grapevines externally free from grapevine trunk disease symptoms

(2016) E. Bruez et al.   AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH

DNA barcoding for biosecurity: case studies from the UK plant protection program

(2016) Jennifer Hodgetts et al.   GENOME

Analysis of the Fungal Diversity in Citrus Leaves with Greasy Spot Disease Symptoms

(2016) Ahmed Abdelfattah et al.   MICROBIAL ECOLOGY

A Metabarcoding Survey on the Fungal Microbiota Associated to the Olive Fruit Fly

(2016) Antonino Malacrinò et al.   MICROBIAL ECOLOGY

Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum

(2016) Mélanie Massonnet et al.   MOLECULAR PLANT PATHOLOGY

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

(2016) Nicholas A. Bokulich et al.   mBio

Variations in Early Response of Grapevine Wood Depending on Wound and Inoculation Combinations with Phaeoacremonium aleophilum and Phaeomoniella chlamydospora

(2016) Romain J. G. Pierron et al.   Frontiers in Plant Science

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

(2015) Abraham Morales-Cruz et al.   BMC GENOMICS

Cadophora species associated with wood-decay of grapevine in North America

(2015) Renaud Travadon et al.   Fungal Biology

Diversity of Diaporthe species associated with wood cankers of fruit and nut crops in northern California

(2015) Daniel P. Lawrence et al.   MYCOLOGIA

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Common foliar fungi ofPopulus trichocarpamodifyMelampsorarust disease severity

(2015) Posy E. Busby et al.   NEW PHYTOLOGIST

Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests

(2015) Bonnie G. Waring et al.   NEW PHYTOLOGIST

Molecular Polymorphism and Phenotypic Diversity in the Eutypa Dieback Pathogen Eutypa lata

(2015) Renaud Travadon et al.   PHYTOPATHOLOGY

Development of a DNA Macroarray for the Detection and Identification of Fungal Pathogens Causing Decline of Young Grapevines

(2015) J. R. Úrbez-Torres et al.   PHYTOPATHOLOGY

Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems

(2015) Mathabatha E. Setati et al.   Frontiers in Microbiology

Synergisms between microbial pathogens in plant disease complexes: a growing trend

(2015) Jay Ram Lamichhane et al.   Frontiers in Plant Science

Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry

(2015) Xiangming Xu et al.   Horticulture Research

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

(2014) Suzanne M. Prober et al.   ECOLOGY LETTERS

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Analyses of the Temporal Dynamics of Fungal Communities Colonizing the Healthy Wood Tissues of Esca Leaf-Symptomatic and Asymptomatic Vines

(2014) Emilie Bruez et al.   PLoS One

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

(2013) Nicholas A. Bokulich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A method to detect and quantify Phaeomoniella chlamydospora and Phaeoacremonium aleophilum DNA in grapevine-wood samples

(2013) Jérôme Pouzoulet et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

DNA barcoding of Mycosphaerella species of quarantine importance to Europe

(2013) W. Quaedvlieg et al.   PERSOONIA

Grapevine Trunk Diseases in British Columbia: Incidence and Characterization of the Fungal Pathogens Associated with Esca and Petri Diseases of Grapevine

(2013) J. R. Úrbez-Torres et al.   PLANT DISEASE

Co-infection by Botryosphaeriaceae andIlyonectriaspp. fungi during propagation causes decline of young grafted grapevines

(2013) M. A. Whitelaw-Weckert et al.   PLANT PATHOLOGY

Detection and quantification ofIlyonectriaspp. associated with black-foot disease of grapevine in nursery soils using multiplex nested PCR and quantitative PCR

(2013) C. Agustí-Brisach et al.   PLANT PATHOLOGY

Monitoring Seasonal Changes in Winery-Resident Microbiota

(2013) Nicholas A. Bokulich et al.   PLoS One

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

(2013) N. A. Bokulich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Illumina metabarcoding of a soil fungal community

(2013) Philipp-André Schmidt et al.   SOIL BIOLOGY & BIOCHEMISTRY

Real-Time PCR Detection of Phaeomoniella chlamydospora and Phaeoacremonium aleophilum

(2012) Maria Teresa Martín et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Grapevine trunk diseases: complex and still poorly understood

(2012) C. Bertsch et al.   PLANT PATHOLOGY

Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi

(2012) L. Kiss   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

Multi-gene analysis and morphology reveal novel Ilyonectria species associated with black foot disease of grapevines

(2011) Ana Cabral et al.   Fungal Biology

Fungal Trunk Pathogens in the Grapevine Propagation Process: Potential Inoculum Sources, Detection, Identification, and Management Strategies

(2011) D. Gramaje et al.   PLANT DISEASE

Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

(2010) J. K. Harris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Phyllosphere microbiology with special reference to diversity and plant genotype

(2008) J.M. Whipps et al.   JOURNAL OF APPLIED MICROBIOLOGY