A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

Comparative transcriptomic analyses ofZymoseptoria triticistrains show complex lifestyle transitions and intraspecific variability in transcription profiles

(2016) Javier Palma-Guerrero et al.   MOLECULAR PLANT PATHOLOGY

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

(2016) Clémence Plissonneau et al.   mBio

Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici

(2016) Megan C. McDonald et al.   G3-Genes Genomes Genetics

Fungal Effectors and Plant Susceptibility

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

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

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

How eukaryotic filamentous pathogens evade plant recognition

(2015) Ely Oliveira-Garcia et al.   CURRENT OPINION IN MICROBIOLOGY

Is Zymoseptoria tritici a hemibiotroph?

(2015) Andrea Sánchez-Vallet et al.   FUNGAL GENETICS AND BIOLOGY

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

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

Genetics of resistance to Zymoseptoria tritici and applications to wheat breeding

(2015) James K.M. Brown 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

Rapid identification of theLeptosphaeria maculansavirulence geneAvrLm2using an intraspecific comparative genomics approach

(2015) Kaveh Ghanbarnia et al.   MOLECULAR PLANT PATHOLOGY

Effector discovery in the fungal wheat pathogenZymoseptoria tritici

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

Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon

(2015) Sarah Maria Schmidt et al.   NEW PHYTOLOGIST

A game of hide and seek between avirulence genesAvrLm4-7andAvrLm3inLeptosphaeria maculans

(2015) Clémence Plissonneau et al.   NEW PHYTOLOGIST

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

(2015) Aoife McLysaght et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Revealing Shared and Distinct Gene Network Organization in Arabidopsis Immune Responses by Integrative Analysis

(2015) Xiaobao Dong 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

Horizontal Gene Transfer in Eukaryotic Plant Pathogens

(2014) Darren Soanes et al.   Annual Review of Phytopathology

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

Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens

(2014) Vivianne G. A. A. Vleeshouwers et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Measuring Quantitative Virulence in the Wheat Pathogen Zymoseptoria tritici Using High-Throughput Automated Image Analysis

(2014) Ethan L. Stewart et al.   PHYTOPATHOLOGY

An Immunity-Triggering Effector from the Barley Smut Fungus Ustilago hordei Resides in an Ustilaginaceae-Specific Cluster Bearing Signs of Transposable Element-Assisted Evolution

(2014) Shawkat Ali et al.   PLoS Pathogens

Duplications and losses in gene families of rust pathogens highlight putative effectors

(2014) Amanda L. Pendleton et al.   Frontiers in Plant Science

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

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

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

Recent Progress in Understanding PAMP- and Effector-Triggered Immunity against the Rice Blast Fungus Magnaporthe oryzae

(2013) Wende Liu et al.   Molecular Plant

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Mechanisms and Evolution of Virulence in Oomycetes

(2012) Rays H.Y. Jiang et al.   Annual Review of Phytopathology

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Zymoseptoria ardabiliae and Z. pseudotritici, two progenitor species of the septoria tritici leaf blotch fungus Z. tritici (synonym: Mycosphaerella graminicola)

(2012) Eva H. Stukenbrock et al.   MYCOLOGIA

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

A Genetic Mechanism for Emergence of Races in Fusarium oxysporum f. sp. lycopersici: Inactivation of Avirulence Gene AVR1 by Transposon Insertion

(2012) Keigo Inami et al.   PLoS One

Defining the Predicted Protein Secretome of the Fungal Wheat Leaf Pathogen Mycosphaerella graminicola

(2012) Alexandre Morais do Amaral et al.   PLoS One

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

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

Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts

(2012) Donald M. Gardiner et al.   PLoS Pathogens

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

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

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Transcriptome analysis of Stagonospora nodorum: gene models, effectors, metabolism and pantothenate dispensability

(2011) SIMON V. S. IPCHO et al.   MOLECULAR PLANT PATHOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Analysis of Two in Planta Expressed LysM Effector Homologs from the Fungus Mycosphaerella graminicola Reveals Novel Functional Properties and Varying Contributions to Virulence on Wheat

(2011) R. Marshall et al.   PLANT PHYSIOLOGY

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

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

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

(2010) Joy Bergelson et al.   NATURE REVIEWS GENETICS

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

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

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

Genome Organization and Evolution of theAVR-PitaAvirulence Gene Family in theMagnaporthe griseaSpecies Complex

(2008) Chang Hyun Khang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Specificity of Incomplete Resistance to Mycosphaerella graminicola in Wheat

(2008) J. E. Krenz et al.   PHYTOPATHOLOGY

Transcriptome content and dynamics at single-nucleotide resolution

(2008) Nicole Cloonan et al.   GENOME BIOLOGY