The genome assembly of the fungal pathogen Pyrenochaeta lycopersici from Single-Molecule Real-Time sequencing sheds new light on its biological complexity

Regulation of proteinaceous effector expression in phytopathogenic fungi

(2017) Kar-Chun Tan et al.   PLoS Pathogens

OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes

(2016) Alison C. Testa et al.   Genome Biology and Evolution

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

(2016) Raúl Castanera et al.   PLoS Genetics

Fungal Effectors and Plant Susceptibility

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

Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

(2015) Joëlle Amselem et al.   BMC GENOMICS

The Genome of the Saprophytic Fungus Verticillium tricorpus Reveals a Complex Effector Repertoire Resembling That of Its Pathogenic Relatives

(2015) Michael F. Seidl et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Sex or no sex: Evolutionary adaptation occurs regardless

(2014) Michael F. Seidl et al.   BIOESSAYS

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici

(2014) Maria Aragona et al.   BMC GENOMICS

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

(2014) Jonathan Grandaubert et al.   BMC GENOMICS

Genetic structure of Italian populations ofPyrenochaeta lycopersici, the causal agent of corky root rot of tomato

(2014) A. Infantino et al.   PLANT PATHOLOGY

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

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

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

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Fungal-specific transcription factorAbPf2activates pathogenicity inAlternaria brassicicola

(2013) Yangrae Cho et al.   PLANT JOURNAL

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

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

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Molecular and functional characterization of an endoglucanase in the phytopathogenic fungus Pyrenochaeta lycopersici

(2011) Maria Teresa Valente et al.   CURRENT GENETICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Cutting the Gordian knot: taking a stab at corky root rot of tomato

(2011) Sophia K. Ekengren   Plant Biotechnology

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

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

(2011) Thierry Rouxel et al.   Nature Communications

Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional chinese medicine

(2011) Peng Zheng et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Accidental Amplification and Inactivation of a Methyltransferase Gene Eliminates Cytosine Methylation in Mycosphaerella graminicola

(2010) Braham Dhillon et al.   GENETICS

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu 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

Transposable Elements and Factors Influencing their Success in Eukaryotes

(2009) E. J. Pritham   JOURNAL OF HEREDITY

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE