Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat

Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome

(2018) Clémence Plissonneau et al.   BMC BIOLOGY

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

(2018) Lukas Meile et al.   NEW PHYTOLOGIST

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

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 transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize

(2017) Chao Wang et al.   NEW PHYTOLOGIST

Skin color variation in Africa

(2017) Hua Tang et al.   SCIENCE

Transposable Elements Direct The Coevolution between Plants and Microbes

(2017) Michael F. Seidl et al.   TRENDS IN GENETICS

Plasticity of the MFS1 Promoter Leads to Multidrug Resistance in the Wheat Pathogen Zymoseptoria tritici

(2017) Selim Omrane et al.   mSphere

Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

(2016) Vahan B. Indjeian et al.   CELL

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

(2016) Luigi Faino et al.   GENOME RESEARCH

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

The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems

(2016) Daniel Croll et al.   MOLECULAR ECOLOGY

Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations

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

Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens

(2016) Michael F. Seidl et al.   PLoS Pathogens

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

(2016) Francisco Salinas et al.   Scientific Reports

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

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

Chromatin-based control of effector gene expression in plant-associated fungi

(2015) Jessica L Soyer et al.   CURRENT OPINION IN PLANT 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

A gene locus for targeted ectopic gene integration in Zymoseptoria tritici

(2015) S. Kilaru et al.   FUNGAL GENETICS AND BIOLOGY

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

(2015) Klaas Schotanus et al.   Epigenetics & Chromatin

A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

(2015) Hude Mao et al.   Nature Communications

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

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

A modelling framework to simulate foliar fungal epidemics using functional–structural plant models

(2014) Guillaume Garin et al.   ANNALS OF BOTANY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Variability of chromosome structure in pathogenic fungi—of ‘ends and odds’

(2014) Jonathan M Galazka et al.   CURRENT OPINION IN MICROBIOLOGY

Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis

(2014) Tetsuya Chujo et al.   MOLECULAR MICROBIOLOGY

A comparison of key aspects of gene regulation inStreptomyces coelicolorandEscherichia coliusing nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

(2014) David A. Romero et al.   MOLECULAR MICROBIOLOGY

Incidence of Cyp51 A Key Mutations in Aspergillus fumigatus—A Study on Primary Clinical Samples of Immunocompromised Patients in the Period of 1995–2013

(2014) Birgit Spiess et al.   PLoS One

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

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

Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans

(2014) Jessica L. Soyer et al.   PLoS Genetics

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

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

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

The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast

(2013) Jessica Chang et al.   PLoS Genetics

The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters

(2013) Lanelle R. Connolly et al.   PLoS Genetics

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

Epigenetic control of transposon transcription and mobility in Arabidopsis

(2012) Etienne Bucher et al.   CURRENT OPINION IN PLANT BIOLOGY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

(2012) Steven R. Eichten et al.   PLoS Genetics

Evidence for Extensive Recent Intron Transposition in Closely Related Fungi

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

Aberrant protein N-glycosylation impacts upon infection-related growth transitions of the haploid plant-pathogenic fungus Mycosphaerella graminicola

(2011) Juliet Motteram et al.   MOLECULAR MICROBIOLOGY

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

R/qtl: high-throughput multiple QTL mapping: Fig. 1.

(2010) Danny Arends et al.   BIOINFORMATICS

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project

(2010) Navreet K Bhullar et al.   BMC PLANT BIOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Linking the emergence of fungal plant diseases with ecological speciation

(2010) Tatiana Giraud et al.   TRENDS IN ECOLOGY & EVOLUTION

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Color me bad: microbial pigments as virulence factors

(2009) George Y. Liu et al.   TRENDS IN MICROBIOLOGY

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

(2008) Z. A. Lewis et al.   GENOME RESEARCH

Adaptive Melanin Response of the Soil Fungus Aspergillus niger to UV Radiation Stress at “Evolution Canyon”, Mount Carmel, Israel

(2008) Natarajan Singaravelan et al.   PLoS One

Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley

(2008) Arnis Druka et al.   THEORETICAL AND APPLIED GENETICS

Adaptive evolution in invasive species

(2008) Peter J. Prentis et al.   TRENDS IN PLANT SCIENCE

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY