Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure

An integrated approach to control the introduced forest pathogen Heterobasidion irregulare in Europe

(2014) P. Gonthier et al.   FORESTRY

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

A First Generation Heterobasidion Hybrid Discovered in Larix lyalli in Montana

(2014) B. Lockman et al.   PLANT DISEASE

Ecological understanding of root-infecting fungi using trait-based approaches

(2014) Carlos A. Aguilar-Trigueros et al.   TRENDS IN PLANT SCIENCE

Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors

(2014) Antoine Persoons et al.   Frontiers in Plant Science

The evolving fungal genome

(2014) Eva H. Stukenbrock et al.   Fungal Biology Reviews

Biology, Epidemiology, and Control ofHeterobasidionSpecies Worldwide

(2013) Matteo Garbelotto et al.   Annual Review of Phytopathology

Tuning a ménage à trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants

(2013) Stephan Greiner et al.   BIOESSAYS

The saprobic and fruiting abilities of the exotic forest pathogen Heterobasidion irregulare may explain its invasiveness

(2013) Luana Giordano et al.   BIOLOGICAL INVASIONS

Transcriptomic profiles ofHeterobasidion annosumunder abiotic stresses and during saprotrophic growth in bark, sapwood and heartwood

(2013) Tommaso Raffaello et al.   ENVIRONMENTAL MICROBIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens

(2013) Eva Holtgrewe Stukenbrock   NEW PHYTOLOGIST

A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum s.s

(2013) Kerstin Dalman et al.   PLoS One

Expression and regulation of genes encoding lignocellulose-degrading activity in the genus Phanerochaete

(2012) Jacqueline MacDonald et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The American forest pathogenHeterobasidion irregularecolonizes unexpected habitats after its introduction in Italy

(2012) Paolo Gonthier et al.   ECOLOGICAL APPLICATIONS

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

(2012) Pablo Cingolani et al.   FLY

Microevolution of Cryptococcus neoformans Driven by Massive Tandem Gene Amplification

(2012) E. W. L. Chow et al.   MOLECULAR BIOLOGY AND EVOLUTION

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

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

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

(2012) Åke Olson et al.   NEW PHYTOLOGIST

A 2nd Generation Linkage Map of Heterobasidion annosum s.l. Based on In Silico Anchoring of AFLP Markers

(2012) Mårten Lind et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Pathogenomics of fungal plant parasites: what have we learnt about pathogenesis?

(2011) Sarah Maria Schmidt et al.   CURRENT OPINION IN PLANT BIOLOGY

Mitochondria and Fungal Pathogenesis: Drug Tolerance, Virulence, and Potential for Antifungal Therapy

(2011) Miguel Shingu-Vazquez et al.   EUKARYOTIC CELL

Amplified fragment length polymorphism and sequence analyses reveal massive gene introgression from the European fungal pathogen Heterobasidion annosum into its introduced congener H. irregulare

(2011) P. GONTHIER et al.   MOLECULAR ECOLOGY

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

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

Multiple Translocation of the AVR-Pita Effector Gene among Chromosomes of the Rice Blast Fungus Magnaporthe oryzae and Related Species

(2011) Izumi Chuma et al.   PLoS Pathogens

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato

(2010) K. DALMAN et al.   MOLECULAR ECOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Adaptive evolution of energy metabolism genes and the origin of flight in bats

(2010) Y.-Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Mitochondrial bioenergetics as a major motive force of speciation

(2009) Moran Gershoni et al.   BIOESSAYS

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

Comparing the influences of ecological and evolutionary factors on the successful invasion of a fungal forest pathogen

(2009) Matteo Garbelotto et al.   BIOLOGICAL INVASIONS

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi

(2009) Hugo Lavoie et al.   CURRENT OPINION IN MICROBIOLOGY

Heterobasidion occidentale sp. nov. and Heterobasidion irregulare nom. nov.: A disposition of North American Heterobasidion biological species

(2009) William J. Otrosina et al.   Fungal Biology

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Rapid emergence of hybrids between the two subspecies ofOphiostoma novo-ulmiwith a high level of pathogenic fitness

(2009) C. M. Brasier et al.   PLANT PATHOLOGY

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

(2009) Andrew J Pask et al.   GENOME BIOLOGY

Relaxation of yeast mitochondrial functions after whole-genome duplication

(2008) H. Jiang et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Evolution of Eukaryotic Transcription Circuits

(2008) B. B. Tuch et al.   SCIENCE

Inferences on the phylogeography of the fungal pathogen Heterobasidion annosum, including evidence of interspecific horizontal genetic transfer and of human-mediated, long-range dispersal

(2007) R.E. Linzer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION