Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation

Variation in recombination rate affects detection of outliers in genome scans under neutrality

(2020) Tom R. Booker et al.   MOLECULAR ECOLOGY

Creating novel specificities in a fungal nonself recognition system by single step homologous recombination events

(2020) Jörg Kämper et al.   NEW PHYTOLOGIST

The Impact of Protein Architecture on Adaptive Evolution

(2019) Ana Filipa Moutinho et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of recombination maps from a single pair of genomes and its application to ancient samples

(2019) Gustavo V. Barroso et al.   PLoS Genetics

Variation of the adaptive substitution rate between species and within genomes

(2019) Ana Filipa Moutinho et al.   EVOLUTIONARY ECOLOGY

Overestimation of the adaptive substitution rate in fluctuating populations

(2018) Marjolaine Rousselle et al.   Biology Letters

Model averaging in ecology: a review of Bayesian, information-theoretic, and tactical approaches for predictive inference

(2018) Carsten F. Dormann et al.   ECOLOGICAL MONOGRAPHS

Positively Selected Effector Genes and Their Contribution to Virulence in the Smut Fungus Sporisorium reilianum

(2018) Gabriel Schweizer et al.   Genome Biology and Evolution

The Core Effector Cce1 is Required for Early Infection of Maize by Ustilago maydis

(2018) Denise Seitner et al.   MOLECULAR PLANT PATHOLOGY

Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization

(2018) Juliana Benevenuto et al.   Frontiers in Microbiology

The ash dieback invasion of Europe was founded by two genetically divergent individuals

(2018) Mark McMullan et al.   Nature Ecology & Evolution

Sporisorium reilianum possesses a pool of effector proteins that modulate virulence on maize

(2018) Hassan Ghareeb et al.   MOLECULAR PLANT PATHOLOGY

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

(2017) Eva H. Stukenbrock et al.   GENETICS

Ustilago maydis effectors and their impact on virulence

(2017) Daniel Lanver et al.   NATURE REVIEWS MICROBIOLOGY

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

(2017) Eva H. Stukenbrock et al.   GENETICS

Population Genomics of Fungal and Oomycete Pathogens

(2016) Niklaus J. Grünwald et al.   Annual Review of Phytopathology

pong: fast analysis and visualization of latent clusters in population genetic data

(2016) Aaron A. Behr et al.   BIOINFORMATICS

Cell biology of corn smut disease — Ustilago maydis as a model for biotrophic interactions

(2016) Alexandra Matei et al.   CURRENT OPINION IN MICROBIOLOGY

A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi

(2016) Julien Y. Dutheil et al.   Genome Biology and Evolution

Characterization of ApB73, a virulence factor important for colonization ofZea maysby the smutUstilago maydis

(2016) Alexandra Stirnberg et al.   MOLECULAR PLANT PATHOLOGY

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

Making sense of genomic islands of differentiation in light of speciation

(2016) Jochen B. W. Wolf et al.   NATURE REVIEWS GENETICS

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis

(2016) Nicolas Galtier   PLoS Genetics

A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem

(2016) Franziska Rabe et al.   eLife

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

(2015) D. Croll et al.   GENETICS

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extreme selective sweeps independently targeted the X chromosomes of the great apes

(2015) Kiwoong Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant domestication through an ecological lens

(2015) Rubén Milla et al.   TRENDS IN ECOLOGY & EVOLUTION

Genetic, evolutionary and plant breeding insights from the domestication of maize

(2015) Sarah Hake et al.   eLife

Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane

(2015) Lucas M. Taniguti et al.   PLoS One

The Relations Between Recombination Rate and Patterns of Molecular Variation and Evolution in Drosophila

(2014) Brian Charlesworth et al.   Annual Review of Genetics

Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae

(2014) Ju Huang et al.   BMC GENETICS

Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut

(2014) Youxiong Que et al.   BMC GENOMICS

MafFilter: a highly flexible and extensible multiple genome alignment files processor

(2014) Julien Y Dutheil et al.   BMC GENOMICS

Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum

(2014) Rahul Sharma et al.   Genome Biology and Evolution

Patterns of Variation at Ustilago maydis Virulence Clusters 2A and 19A Largely Reflect the Demographic History of Its Populations

(2014) Ronny Kellner et al.   PLoS One

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

Characterization of the Largest Effector Gene Cluster of Ustilago maydis

(2014) Thomas Brefort et al.   PLoS Pathogens

Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors

(2014) Jana Sperschneider et al.   Frontiers in Plant Science

GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

(2013) Yann Lesecque et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus

(2013) Wenming Zheng et al.   Nature Communications

Compatibility in the Ustilago maydis–Maize Interaction Requires Inhibition of Host Cysteine Proteases by the Fungal Effector Pit2

(2013) André N. Mueller et al.   PLoS Pathogens

Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi

(2012) Felix Horns et al.   Genome Biology and Evolution

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

(2012) J. D. Laurie et al.   PLANT CELL

The Ustilago maydis Effector Pep1 Suppresses Plant Immunity by Inhibition of Host Peroxidase Activity

(2012) Christoph Hemetsberger et al.   PLoS Pathogens

A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

(2012) Eva H. Stukenbrock et al.   PLoS Pathogens

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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

(2011) H. Li   BIOINFORMATICS

Quantifying the Variation in the Effective Population Size Within a Genome

(2011) Toni I. Gossmann et al.   GENETICS

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

Two linked genes encoding a secreted effector and a membrane protein are essential for Ustilago maydis-induced tumour formation

(2011) Gunther Doehlemann et al.   MOLECULAR MICROBIOLOGY

A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors inMelampsora larici-populina(Poplar Leaf Rust)

(2011) Stéphane Hacquard et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison

(2010) J. Schirawski et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Domestication and plant genomes

(2009) Haibao Tang et al.   CURRENT OPINION IN PLANT BIOLOGY

Historical Divergence and Gene Flow in the Genus Zea

(2009) J. Ross-Ibarra et al.   GENETICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

A comparative view of the evolution of grasses under domestication

(2009) Sylvain Glémin et al.   NEW PHYTOLOGIST

Pep1, a Secreted Effector Protein of Ustilago maydis, Is Required for Successful Invasion of Plant Cells

(2009) Gunther Doehlemann et al.   PLoS Pathogens

RAPID SPECIATION FOLLOWING RECENT HOST SHIFTS IN THE PLANT PATHOGENIC FUNGUS RHYNCHOSPORIUM

(2008) Pascal L. Zaffarano et al.   EVOLUTION

Sex in smut fungi: Structure, function and evolution of mating-type complexes

(2008) Guus Bakkeren et al.   FUNGAL GENETICS AND BIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

PEDANT covers all complete RefSeq genomes

(2008) M. C. Walter et al.   NUCLEIC ACIDS RESEARCH

Ustilago maydis populations tracked maize through domestication and cultivation in the Americas

(2008) A. B Munkacsi et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES