Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

(2018) Lamprinos Frantzeskakis et al.   BMC GENOMICS

Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen

(2018) Norfarhan Mohd-Assaad et al.   Genome Biology and Evolution

Genome-wide evidence for divergent selection between populations of a major agricultural pathogen

(2018) Fanny E. Hartmann et al.   MOLECULAR ECOLOGY

Evolutionary analyses of the avirulence effector AvrStb6 in global populations of Zymoseptoria tritici identify candidate amino acids involved in recognition

(2018) Patrick C. Brunner et al.   MOLECULAR PLANT PATHOLOGY

Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance

(2018) Gerrit H. J. Kema et al.   NATURE GENETICS

ToxA is present in the United States Bipolaris sorokiniana population and is a significant virulence factor on wheat harboring Tsn1

(2018) Timothy L Friesen et al.   PLANT DISEASE

Multinucleotide mutations cause false inferences of lineage-specific positive selection

(2018) Aarti Venkat et al.   Nature Ecology & Evolution

The need for speed: compartmentalized genome evolution in filamentous phytopathogens

(2018) Lamprinos Frantzeskakis et al.   MOLECULAR PLANT PATHOLOGY

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

(2017) H. Badouin et al.   MOLECULAR ECOLOGY

Nature's genetic screens: using genome-wide association studies for effector discovery

(2017) Andrea Sánchez-Vallet et al.   MOLECULAR PLANT PATHOLOGY

A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene

(2017) Ziming Zhong et al.   NEW PHYTOLOGIST

Reference Quality Genome Assemblies of Three Parastagonospora nodorum Isolates Differing in Virulence on Wheat

(2017) Jonathan K. Richards et al.   G3-Genes Genomes Genetics

Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements

(2016) Kentaro Yoshida et al.   BMC GENOMICS

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

(2016) Luigi Faino et al.   GENOME RESEARCH

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

SnTox1, a Parastagonospora nodorum necrotrophic effector, is a dual-function protein that facilitates infection while protecting from wheat-produced chitinases

(2016) Zhaohui Liu et al.   NEW PHYTOLOGIST

Validation of Genome-Wide Association Studies as a Tool to Identify Virulence Factors inParastagonospora nodorum

(2016) Yuanyuan Gao et al.   PHYTOPATHOLOGY

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

(2016) Robert A. Syme et al.   PLoS One

GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction

(2016) You Tang et al.   Plant Genome

The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease

(2016) G. Shi et al.   Science Advances

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen

(2015) D. Croll et al.   GENETICS

Identification and Characterization of the SnTox6-Snn6 Interaction in the Parastagonospora nodorum–Wheat Pathosystem

(2015) Y. Gao et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Filamentous pathogen effector functions: of pathogens, hosts and microbiomes

(2014) Hanna Rovenich et al.   CURRENT OPINION IN PLANT BIOLOGY

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Filamentous plant pathogen effectors in action

(2013) Martha C. Giraldo et al.   NATURE REVIEWS MICROBIOLOGY

Global diversity and distribution of three necrotrophic effectors inPhaeosphaeria nodorumand related species

(2013) Megan C. McDonald et al.   NEW PHYTOLOGIST

Genes Conferring Sensitivity to Stagonospora nodorum Necrotrophic Effectors in Stagonospora Nodorum Blotch-Susceptible U.S. Wheat Cultivars

(2013) Matthew Bertucci et al.   PLANT DISEASE

Resequencing and Comparative Genomics of Stagonospora nodorum : Sectional Gene Absence and Effector Discovery

(2013) Robert Andrew Syme et al.   G3-Genes Genomes Genetics

Stagonospora nodorum: From Pathology to Genomics and Host Resistance

(2012) Richard P. Oliver et al.   Annual Review of Phytopathology

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

SnTox5-Snn5: a novelStagonospora nodorumeffector-wheat gene interaction and its relationship with the SnToxA-Tsn1and SnTox3-Snn3-B1interactions

(2012) Timothy l. Friesen et al.   MOLECULAR PLANT PATHOLOGY

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Novel Necrotrophic Effectors from Stagonospora nodorum and Corresponding Host Sensitivities in Winter Wheat Germplasm in the Southeastern United States

(2012) A. D. Crook et al.   PHYTOPATHOLOGY

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

The Cysteine Rich Necrotrophic Effector SnTox1 Produced by Stagonospora nodorum Triggers Susceptibility of Wheat Lines Harboring Snn1

(2012) Zhaohui Liu et al.   PLoS Pathogens

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Pervasive Multinucleotide Mutational Events in Eukaryotes

(2011) Daniel R. Schrider et al.   CURRENT BIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

(2011) Stephen B. Goodwin et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

New developments in pathogenicity and virulence of necrotrophs

(2010) Richard P Oliver et al.   CURRENT OPINION IN PLANT BIOLOGY

Plant immunity: towards an integrated view of plant–pathogen interactions

(2010) Peter N. Dodds et al.   NATURE REVIEWS GENETICS

Two putatively homoeologous wheat genes mediate recognition of SnTox3 to confer effector-triggered susceptibility to Stagonospora nodorum

(2010) Zengcui Zhang et al.   PLANT JOURNAL

A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens

(2010) J. D. Faris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants

(2010) R. de Jonge et al.   SCIENCE

Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

(2010) Eva H. Stukenbrock et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Early molecular events in PAMP-triggered immunity

(2009) Cyril Zipfel   CURRENT OPINION IN PLANT BIOLOGY

Host–pathogen warfare at the plant cell wall

(2009) Kian Hématy et al.   CURRENT OPINION IN PLANT BIOLOGY

Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists

(2009) Gabriela Aguileta et al.   INFECTION GENETICS AND EVOLUTION

Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini

(2009) L. G. Barrett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population Genetics of Fungal and Oomycete Effectors Involved in Gene-for-Gene Interactions

(2009) Eva H. Stukenbrock et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

SnTox3 Acts in Effector Triggered Susceptibility to Induce Disease on Wheat Carrying the Snn3 Gene

(2009) Zhaohui Liu et al.   PLoS Pathogens

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Development, identification, and validation of markers for marker-assisted selection against the Stagonospora nodorum toxin sensitivity genes Tsn1 and Snn2 in wheat

(2008) Zengcui Zhang et al.   MOLECULAR BREEDING