Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

(2015) Robert King et al.   BMC GENOMICS

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

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

An update to polyketide synthase and non-ribosomal synthetase genes and nomenclature in Fusarium

(2015) Frederik T. Hansen et al.   FUNGAL GENETICS AND BIOLOGY

Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity

(2015) Jana Sperschneider et al.   Genome Biology and Evolution

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

(2015) Sven Warris et al.   PLoS One

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

(2015) Luigi Faino et al.   mBio

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

(2015) Klaas Schotanus et al.   Epigenetics & Chromatin

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Relocation of genes generates non-conserved chromosomal segments in Fusarium graminearum that show distinct and co-regulated gene expression patterns

(2014) Chunzhao Zhao et al.   BMC GENOMICS

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

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

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

The compositional mosaic of Fusarium species and their mycotoxins in unprocessed cereals, food and feed products in Belgium

(2014) Adriaan Vanheule et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation

(2014) Xiao Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolving fungal genome

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

FusariumPathogenomics

(2013) Li-Jun Ma et al.   Annual Review of Microbiology

RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum

(2013) Chunzhao Zhao et al.   BMC GENOMICS

EBR1genomic expansion and its role in virulence ofFusariumspecies

(2013) Wilfried Jonkers et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria

(2013) Kerry O’Donnell et al.   FUNGAL GENETICS AND BIOLOGY

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

(2013) Eva Holtgrewe Stukenbrock   NEW PHYTOLOGIST

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes 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

gff2sequence, a new user friendly tool for the generation of genomic sequences

(2013) Salvatore Camiolo et al.   BioData Mining

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer

(2012) Jinnan Hu et al.   BMC GENOMICS

Sex in Cheese: Evidence for Sexuality in the Fungus Penicillium roqueforti

(2012) Jeanne Ropars et al.   PLoS One

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

EBR1, a Novel Zn2Cys6Transcription Factor, Affects Virulence and Apical Dominance of the Hyphal Tip inFusarium graminearum

(2011) Chunzhao Zhao et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

(2011) Thierry Rouxel et al.   Nature Communications

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

The Stealth Episome: Suppression of Gene Expression on the Excised Genomic Island PPHGI-1 from Pseudomonas syringae pv. phaseolicola

(2011) Scott A. C. Godfrey et al.   PLoS Pathogens

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

(2010) A. John Clutterbuck   FUNGAL GENETICS AND BIOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fusarium head blight (FHB) in Flanders: population diversity, inter-species associations and DON contamination in commercial winter wheat varieties

(2009) K. Audenaert et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

Meiosis Drives Extraordinary Genome Plasticity in the Haploid Fungal Plant Pathogen Mycosphaerella graminicola

(2009) Alexander H. J. Wittenberg et al.   PLoS One

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

(2008) James K Hane et al.   BMC BIOINFORMATICS

Fusarium Populations on Chinese Barley Show a Dramatic Gradient in Mycotoxin Profiles

(2008) L. Yang et al.   PHYTOPATHOLOGY