Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome

A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

(2017) Fanny E Hartmann et al.   ISME Journal

Comparative Transcriptome Analyses inZymoseptoria triticiReveal Significant Differences in Gene Expression Among Strains During Plant Infection

(2017) Javier Palma-Guerrero et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene

(2017) Ziming Zhong et al.   NEW PHYTOLOGIST

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

(2017) Nicholas J. Croucher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes

(2016) Claudio A. Valero-Jiménez et al.   BMC GENOMICS

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

(2016) Sean Walkowiak et al.   BMC GENOMICS

Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

(2016) Riccardo Baroncelli et al.   BMC GENOMICS

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

(2016) Clémence Plissonneau et al.   mBio

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

Fungal Effectors and Plant Susceptibility

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

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

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

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

Genetics of resistance to Zymoseptoria tritici and applications to wheat breeding

(2015) James K.M. Brown et al.   FUNGAL GENETICS AND BIOLOGY

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

(2015) D. Croll et al.   GENETICS

Effector discovery in the fungal wheat pathogenZymoseptoria tritici

(2015) Amir Mirzadi Gohari et al.   MOLECULAR PLANT PATHOLOGY

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

Transcriptome and Metabolite Profiling of the Infection Cycle ofZymoseptoria triticion Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition

(2015) Jason J. Rudd et al.   PLANT PHYSIOLOGY

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

RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements

(2015) Jonathan Grandaubert et al.   G3-Genes Genomes Genetics

Advances and Challenges in Computational Prediction of Effectors from Plant Pathogenic Fungi

(2015) Jana Sperschneider et al.   PLoS Pathogens

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

Decoding long nanopore sequencing reads of natural DNA

(2014) Andrew H Laszlo et al.   NATURE BIOTECHNOLOGY

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

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

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

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 wheat–Septoria conflict: a new front opening up?

(2014) Aoife O’Driscoll et al.   TRENDS IN PLANT SCIENCE

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

(2014) Kevin Cheeseman et al.   Nature Communications

Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic Fungus Zymoseptoria tritici

(2014) Mark H. Lendenmann et al.   G3-Genes Genomes Genetics

Gene Copy-Number Alterations: A Cost-Benefit Analysis

(2013) Yun-Chi Tang et al.   CELL

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

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

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

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

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

(2012) Pablo Cingolani et al.   FLY

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Evidence for Extensive Recent Intron Transposition in Closely Related Fungi

(2011) Stefano F.F. Torriani et al.   CURRENT BIOLOGY

Horizontal gene transfer in fungi

(2011) David A. Fitzpatrick   FEMS MICROBIOLOGY LETTERS

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

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Analysis of Two in Planta Expressed LysM Effector Homologs from the Fungus Mycosphaerella graminicola Reveals Novel Functional Properties and Varying Contributions to Virulence on Wheat

(2011) R. Marshall et al.   PLANT PHYSIOLOGY

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

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

QoI resistance emerged independently at least 4 times in European populations ofMycosphaerella graminicola

(2008) Stefano FF Torriani et al.   PEST MANAGEMENT SCIENCE