Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum

(2019) Ayako Tsushima et al.   Genome Biology and Evolution

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

(2018) Paula Moolhuijzen et al.   BMC GENOMICS

Just the surface: advances in the discovery and characterization of necrotrophic wheat effectors

(2018) Megan C McDonald et al.   CURRENT OPINION IN MICROBIOLOGY

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

(2018) Manuel Tardaguila et al.   GENOME RESEARCH

ToxA is present in the United States Bipolaris sorokiniana population and is a significant virulence factor on wheat harboring Tsn1

(2018) Timothy L Friesen et al.   PLANT DISEASE

NLR surveillance of essential SEC-9 SNARE proteins induces programmed cell death upon allorecognition in filamentous fungi

(2018) Jens Heller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

The need for speed: compartmentalized genome evolution in filamentous phytopathogens

(2018) Lamprinos Frantzeskakis et al.   MOLECULAR PLANT PATHOLOGY

Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element

(2018) Paula M. Moolhuijzen et al.   PLoS One

Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

(2018) David J. Winter et al.   PLoS Genetics

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

(2017) Fanny E Hartmann et al.   ISME Journal

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

PacBio Sequencing Reveals Transposable Elements as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae

(2017) Jiandong Bao et al.   Molecular Plant

The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana

(2017) Megan C. McDonald et al.   MOLECULAR PLANT PATHOLOGY

Reference Quality Genome Assemblies of Three Parastagonospora nodorum Isolates Differing in Virulence on Wheat

(2017) Jonathan K. Richards et al.   G3-Genes Genomes Genetics

Horizontal transfers of transposable elements in eukaryotes: The flying genes

(2016) Olivier Panaud   COMPTES RENDUS BIOLOGIES

Recombination-independent recognition of DNA homology for repeat-induced point mutation

(2016) Eugene Gladyshev et al.   CURRENT GENETICS

Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi

(2016) Marina Marcet-Houben et al.   FUNGAL GENETICS AND BIOLOGY

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

(2016) Luigi Faino et al.   GENOME RESEARCH

Continuous Influx of Genetic Material from Host to Virus Populations

(2016) Clément Gilbert et al.   PLoS Genetics

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi

(2015) Jeanne Ropars et al.   CURRENT BIOLOGY

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

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

A ToxA-like protein from Cochliobolus heterostrophus induces light-dependent leaf necrosis and acts as a virulence factor with host selectivity on maize

(2015) Shunwen Lu et al.   FUNGAL GENETICS AND BIOLOGY

Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts

(2015) Souhir Marsit et al.   MOLECULAR BIOLOGY AND EVOLUTION

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Extrachromosomal circular DNA is common in yeast

(2015) Henrik D. Møller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

Spy: A New Group of Eukaryotic DNA Transposons without Target Site Duplications

(2014) Min-Jin Han et al.   Genome Biology and Evolution

Diversity and Variability of NOD-Like Receptors in Fungi

(2014) Witold Dyrka et al.   Genome Biology and Evolution

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Multiple recent horizontal transfers of a large genomic region in cheese making fungi

(2014) Kevin Cheeseman et al.   Nature Communications

Direct recognition of homology between double helices of DNA in Neurospora crassa

(2014) Eugene Gladyshev et al.   Nature Communications

Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons

(2014) Clément Gilbert et al.   Nature Communications

The Evolution of Fungal Metabolic Pathways

(2014) Jennifer H. Wisecaver et al.   PLoS Genetics

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

Global diversity and distribution of three necrotrophic effectors inPhaeosphaeria nodorumand related species

(2013) Megan C. McDonald et al.   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

Resequencing and Comparative Genomics of Stagonospora nodorum : Sectional Gene Absence and Effector Discovery

(2013) Robert Andrew Syme et al.   G3-Genes Genomes Genetics

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

(2013) Bradford J. Condon et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster

(2012) Matthew A. Campbell et al.   Genome Biology and Evolution

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Horizontal Transfer of Antibiotic Resistance Genes on Abiotic Touch Surfaces: Implications for Public Health

(2012) S. L. Warnes et al.   mBio

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Nongenetic Reprogramming of a Fungal Highly Reducing Polyketide Synthase

(2011) Ahmed A. Yakasai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae

(2011) Anthony R. Borneman et al.   PLoS Genetics

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

(2010) Jason C. Slot et al.   CURRENT BIOLOGY

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Host-selective toxins, Ptr ToxA and Ptr ToxB, as necrotrophic effectors in the Pyrenophora tritici-repentis-wheat interaction

(2010) Lynda M. Ciuffetti et al.   NEW PHYTOLOGIST

Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

(2010) M.M. Aveskamp et al.   STUDIES IN MYCOLOGY

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

(2009) M. Novo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acquisition of prokaryotic genes by fungal genomes

(2009) Marina Marcet-Houben et al.   TRENDS IN GENETICS

Prevalence of ToxA-sensitive alleles of the wheat geneTsn1in Australian and Chinese wheat cultivars

(2009) Richard P. Oliver et al.   Crop & Pasture Science

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

(2008) James K Hane et al.   BMC BIOINFORMATICS

Genome characterization ofPyrenophora tritici-repentisisolates reveals high plasticity and independent chromosomal location ofToxAandToxB

(2008) R. ABOUKHADDOUR et al.   MOLECULAR PLANT PATHOLOGY

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY