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

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

A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

(2017) Fanny E Hartmann et al.   ISME Journal

Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen

(2017) Fanny E. Hartmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) H. Badouin et al.   MOLECULAR ECOLOGY

Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew

(2017) Chloé E. L. Delmas et al.   MOLECULAR ECOLOGY

Fungal adaptation to contemporary fungicide applications: the case of Botrytis cinerea populations from Champagne vineyards (France)

(2017) A.-S. Walker et al.   MOLECULAR ECOLOGY

Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici

(2017) Ethan l. Stewart et al.   MOLECULAR PLANT PATHOLOGY

Comparative Transcriptome Analyses inZymoseptoria triticiReveal Significant Differences in Gene Expression Among Strains During Plant Infection

(2017) Javier Palma-Guerrero et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

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

The Evolutionary Consequences of Stepwise Infection Processes

(2017) Matthew D. Hall et al.   TRENDS IN ECOLOGY & EVOLUTION

A survey of methods and tools to detect recent and strong positive selection

(2017) Pavlos Pavlidis et al.   Journal of Biological Research-Thessaloniki

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici

(2016) M H Lendenmann et al.   HEREDITY

Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

(2016) Sara Branco et al.   MOLECULAR ECOLOGY

Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations

(2016) Norfarhan Mohd-Assaad et al.   MOLECULAR ECOLOGY

Mutations in the CYP51 gene reduce DMI sensitivity in Parastagonospora nodorum populations in Europe and China

(2016) Danilo AS Pereira et al.   PEST MANAGEMENT SCIENCE

Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security

(2016) Bruce A. McDonald et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reduced Virulence of Azoxystrobin-Resistant Zymoseptoria tritici Populations in Greenhouse Assays

(2016) Christina H. Hagerty et al.   PHYTOPATHOLOGY

A Global Analysis of CYP51 Diversity and Azole Sensitivity in Rhynchosporium commune

(2016) Patrick C. Brunner et al.   PHYTOPATHOLOGY

Population Genomics for Understanding Adaptation in Wild Plant Species

(2015) Detlef Weigel et al.   Annual Review of Genetics

Fungal Effectors and Plant Susceptibility

(2015) Libera Lo Presti et al.   Annual Review of Plant Biology

The impact of Septoria tritici Blotch disease on wheat: An EU perspective

(2015) Helen Fones et al.   FUNGAL GENETICS AND BIOLOGY

QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici

(2015) Mark H. Lendenmann et al.   FUNGAL GENETICS AND BIOLOGY

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

(2015) D. Croll et al.   GENETICS

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Genomic Signature of Selective Sweeps Illuminates Adaptation ofMedicago truncatulato Root-Associated Microorganisms

(2015) Maxime Bonhomme et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic isolation between two recently diverged populations of a symbiotic fungus

(2015) Sara Branco et al.   MOLECULAR ECOLOGY

Effector discovery in the fungal wheat pathogenZymoseptoria tritici

(2015) Amir Mirzadi Gohari et al.   MOLECULAR PLANT PATHOLOGY

Emergence and early evolution of fungicide resistance in North American populations ofZymoseptoria tritici

(2015) L. K. Estep et al.   PLANT PATHOLOGY

Transcriptome and Metabolite Profiling of the Infection Cycle ofZymoseptoria triticion Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition

(2015) Jason J. Rudd et al.   PLANT PHYSIOLOGY

RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements

(2015) Jonathan Grandaubert et al.   G3-Genes Genomes Genetics

Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola)

(2015) Stephan Poppe et al.   PLoS Pathogens

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

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

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

(2014) Luke M Evans et al.   NATURE GENETICS

The wheat–Septoria conflict: a new front opening up?

(2014) Aoife O’Driscoll et al.   TRENDS IN PLANT SCIENCE

Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic Fungus Zymoseptoria tritici

(2014) Mark H. Lendenmann et al.   G3-Genes Genomes Genetics

Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

(2014) Saber Qanbari et al.   PLoS Genetics

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Local adaptation and evolutionary potential along a temperature gradient in the fungal pathogenRhynchosporium commune

(2013) Tryggvi S. Stefansson et al.   Evolutionary Applications

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Coevolution and Life Cycle Specialization of Plant Cell Wall Degrading Enzymes in a Hemibiotrophic Pathogen

(2013) Patrick C. Brunner et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

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

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Association between Virulence and Triazole Tolerance in the Phytopathogenic Fungus Mycosphaerella graminicola

(2013) Lina Yang et al.   PLoS One

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

(2013) Daniel Croll et al.   PLoS Genetics

The impact of equilibrium assumptions on tests of selection

(2013) Jessica L. Crisci et al.   Frontiers in Genetics

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

(2012) Mathieu Gautier et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Update on mechanisms of azole resistance inMycosphaerella graminicolaand implications for future control

(2012) Hans J Cools et al.   PEST MANAGEMENT SCIENCE

Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species

(2012) E. H. Stukenbrock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

(2012) D. J. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

(2012) R. de Jonge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

The Emergence of Ug99 Races of the Stem Rust Fungus is a Threat to World Wheat Production

(2011) Ravi P. Singh et al.   Annual Review of Phytopathology

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Evidence for Extensive Recent Intron Transposition in Closely Related Fungi

(2011) Stefano F.F. Torriani et al.   CURRENT BIOLOGY

How filamentous pathogens co-opt plants: the ins and outs of fungal effectors

(2011) Ronnie de Jonge et al.   CURRENT OPINION IN PLANT BIOLOGY

Genetic structure and local adaptation of European wheat yellow rust populations: the role of temperature-specific adaptation

(2011) Mamadou Mboup et al.   Evolutionary Applications

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

(2011) E. H. Stukenbrock et al.   GENOME RESEARCH

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Thermal adaptation in the fungal pathogen Mycosphaerella graminicola

(2011) JIASUI ZHAN et al.   MOLECULAR ECOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

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

Diversification and evolution of the avirulence gene AVR-Pita1 in field isolates of Magnaporthe oryzae

(2010) Yuntao Dai et al.   FUNGAL GENETICS AND BIOLOGY

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Sugar transporters for intercellular exchange and nutrition of pathogens

(2010) Li-Qing Chen et al.   NATURE

A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis

(2010) Ramon Wahl et al.   PLOS BIOLOGY

Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants

(2010) Angela P. Van de Wouw et al.   PLoS Pathogens

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

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Origins of Plant Pathogens in Agro-Ecosystems

(2008) Eva H. Stukenbrock et al.   Annual Review of Phytopathology

Evolution of the CYP51 gene in Mycosphaerella graminicola: evidence for intragenic recombination and selective replacement

(2008) P. C. BRUNNER et al.   MOLECULAR PLANT PATHOLOGY

QoI resistance emerged independently at least 4 times in European populations ofMycosphaerella graminicola

(2008) Stefano FF Torriani et al.   PEST MANAGEMENT SCIENCE