Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae

Recurrent evolution of vertebrate transcription factors by transposase capture

(2021) Rachel L. Cosby et al.   SCIENCE

Telomeres and a repeat‐rich chromosome encode effector gene clusters in plant pathogenicColletotrichumfungi

(2021) Pamela Gan et al.   ENVIRONMENTAL MICROBIOLOGY

A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici

(2020) Thomas Badet et al.   BMC BIOLOGY

Contribution of unfixed transposable element insertions to human regulatory variation

(2020) Clément Goubert et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

(2020) Vasavi Sundaram et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data

(2020) Arnold Kuzniar et al.   PeerJ

Subtelomeres as Specialized Chromatin Domains

(2020) Antoine Hocher et al.   BIOESSAYS

Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis

(2020) Mihaela Ola et al.   GENOME RESEARCH

Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective

(2020) Patrick H. Maxwell   Mobile DNA

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

The rise and fall of genes: origins and functions of plant pathogen pangenomes

(2020) Thomas Badet et al.   CURRENT OPINION IN PLANT BIOLOGY

Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

(2020) Jae Young Choi et al.   PLoS Genetics

Comparative genomics reveals the in planta‐ secreted Verticillium dahliae Av2 effector protein recognized in tomato plants that carry the V2 resistance locus

(2020) Edgar A. Chavarro‐Carrero et al.   ENVIRONMENTAL MICROBIOLOGY

Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model

(2020) David E. Torres et al.   Fungal Biology Reviews

Multiple wheat genomes reveal global variation in modern breeding

(2020) Sean Walkowiak et al.   NATURE

A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen

(2020) David E Cook et al.   eLife

Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice

(2019) Alexandre P. Marand et al.   PLANT CELL

Fine-scale characterization of genomic structural variation in the human genome reveals adaptive and biomedically relevant hotspots

(2019) Yen-Lung Lin et al.   Genome Biology and Evolution

Diversity of cytosine methylation across the fungal tree of life

(2019) Adam J. Bewick et al.   Nature Ecology & Evolution

Structural variants in 3000 rice genomes

(2019) Roven Rommel Fuentes et al.   GENOME RESEARCH

Rapid evolution in plant–microbe interactions – a molecular genomics perspective

(2019) Lamprinos Frantzeskakis et al.   NEW PHYTOLOGIST

Destabilization of chromosome structure by histone H3 lysine 27 methylation

(2019) Mareike Möller et al.   PLoS Genetics

Dynamic virulence‐related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation

(2019) Jasper R. L. Depotter et al.   MOLECULAR ECOLOGY

Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software

(2019) Daniel L. Cameron et al.   Nature Communications

Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen

(2019) Simone Fouché et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stronger When Together: Clustering of Plant NLR Disease resistance Genes

(2019) Solveig van Wersch et al.   TRENDS IN PLANT SCIENCE

The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations

(2019) Stephanie van Wyk et al.   PeerJ

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

(2018) Clémence Plissonneau et al.   BMC BIOLOGY

Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat

(2018) Parvathy Krishnan et al.   BMC BIOLOGY

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

(2018) Lamprinos Frantzeskakis et al.   BMC GENOMICS

The birth and death of effectors in rapidly evolving filamentous pathogen genomes

(2018) Simone Fouché et al.   CURRENT OPINION IN MICROBIOLOGY

Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss

(2018) Xiaoqian Shi-Kunne et al.   ENVIRONMENTAL MICROBIOLOGY

Transposable elements shape the human proteome landscape via formation of cis -acting upstream open reading frames

(2018) Shohei Kitano et al.   GENES TO CELLS

The impact of transposable elements in adaptive evolution

(2018) Lukas Schrader et al.   MOLECULAR ECOLOGY

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

RNAi is a critical determinant of centromere evolution in closely related fungi

(2018) Vikas Yadav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Computational tools to unmask transposable elements

(2018) Patricia Goerner-Potvin et al.   NATURE REVIEWS GENETICS

Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

(2018) Antoine Hocher et al.   GENOME RESEARCH

The need for speed: compartmentalized genome evolution in filamentous phytopathogens

(2018) Lamprinos Frantzeskakis et al.   MOLECULAR PLANT PATHOLOGY

Origin and evolution of the plant immune system

(2018) Guan-Zhu Han   NEW PHYTOLOGIST

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

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

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

(2017) Fanny E Hartmann et al.   ISME Journal

Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen

(2017) Fanny E. Hartmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Verticillium dahliaeLysM effectors differentially contribute to virulence on plant hosts

(2017) Anja Kombrink et al.   MOLECULAR PLANT PATHOLOGY

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Evolution and genome architecture in fungal plant pathogens

(2017) Mareike Möller et al.   NATURE REVIEWS MICROBIOLOGY

Transposable Elements Direct The Coevolution between Plants and Microbes

(2017) Michael F. Seidl et al.   TRENDS IN GENETICS

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution

(2017) Yuh Chwen G Lee et al.   eLife

The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens

(2016) Andrea Sánchez-Vallet et al.   Annual Review of Phytopathology

Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements

(2016) Kentaro Yoshida et al.   BMC GENOMICS

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

How retrotransposons shape genome regulation

(2016) Paolo Mita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads

(2016) Houxiang Kang et al.   DNA RESEARCH

Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements

(2016) Amir Szitenberg et al.   Genome Biology and Evolution

A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi

(2016) Julien Y. Dutheil et al.   Genome Biology and Evolution

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

(2016) Luigi Faino et al.   GENOME RESEARCH

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

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

(2016) Clémence Plissonneau et al.   mBio

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

(2016) Raúl Castanera et al.   PLoS Genetics

Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens

(2016) Michael F. Seidl et al.   PLoS Pathogens

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

Understanding Plant Immunity as a Surveillance System to Detect Invasion

(2015) David E. Cook et al.   Annual Review of Phytopathology

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

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 two-speed genomes of filamentous pathogens: waltz with plants

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

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

(2015) Benoît Piégu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

Fate of a mutation in a fluctuating environment

(2015) Ivana Cvijović et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Wham: Identifying Structural Variants of Biological Consequence

(2015) Zev N. Kronenberg et al.   PLoS Computational Biology

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Sex or no sex: Evolutionary adaptation occurs regardless

(2014) Michael F. Seidl et al.   BIOESSAYS

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu 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

Filamentous pathogen effector functions: of pathogens, hosts and microbiomes

(2014) Hanna Rovenich et al.   CURRENT OPINION IN PLANT BIOLOGY

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

VerticilliumSystematics and Evolution: How Confusion Impedes Verticillium Wilt Management and How to Resolve It

(2014) Patrik Inderbitzin et al.   PHYTOPATHOLOGY

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

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

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Genomes of Ashbya Fungi Isolated from Insects Reveal Four Mating-Type Loci, Numerous Translocations, Lack of Transposons, and Distinct Gene Duplications

(2013) Fred S. Dietrich et al.   G3-Genes Genomes Genetics

Loss and Retention of RNA Interference in Fungi and Parasites

(2013) Francisco E. Nicolás et al.   PLoS Pathogens

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

(2012) Stefan G Amyotte et al.   BMC GENOMICS

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

(2012) Pablo Cingolani et al.   FLY

The peppered moth and industrial melanism: evolution of a natural selection case study

(2012) L M Cook et al.   HEREDITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transposon integration enhances expression of stress response genes

(2012) Gang Feng et al.   NUCLEIC ACIDS RESEARCH

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

(2012) R. de Jonge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The struggle for life of the genome's selfish architects

(2011) Aurélie Hua-Van et al.   Biology Direct

Causes and Consequences of Genome Expansion in Fungi

(2011) Yogeshwar D. Kelkar et al.   Genome Biology and Evolution

LTR Retrotransposons in Fungi

(2011) Anna Muszewska 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

A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 Elements

(2011) Jason E. Chan et al.   PLoS Genetics

Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens

(2011) Steven J. Klosterman et al.   PLoS Pathogens

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Transposon impala Is Activated by Low Temperatures: Use of a Controlled Transposition System To Identify Genes Critical for Viability of Aspergillus fumigatus

(2010) Paul D. Carr et al.   EUKARYOTIC CELL

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

(2010) A. John Clutterbuck   FUNGAL GENETICS AND BIOLOGY

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Diversity, Pathogenicity, and Management of Verticillium Species

(2009) Steven J. Klosterman et al.   Annual Review of Phytopathology

CROC: finding chromosomal clusters in eukaryotic genomes

(2009) M. Pignatelli et al.   BIOINFORMATICS

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

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

Is evolution Darwinian or/and Lamarckian?

(2009) Eugene V Koonin et al.   Biology Direct

Molecular domestication of transposable elements: From detrimental parasites to useful host genes

(2009) L. Sinzelle et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe

(2009) Y. Guo et al.   GENOME RESEARCH

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Repeat-Induced Point Mutation (RIP) as an Alternative Mechanism of Evolution Toward Virulence inLeptosphaeria maculans

(2009) Isabelle Fudal et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Mechanisms of change in gene copy number

(2009) P. J. Hastings et al.   NATURE REVIEWS GENETICS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Dynamics of transposable elements: towards a community ecology of the genome

(2009) Samuel Venner et al.   TRENDS IN GENETICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Retrotransposon Tf1 Is Targeted to Pol II Promoters by Transcription Activators

(2008) Young-Eun Leem et al.   MOLECULAR CELL

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Stress-induced mobility of OPHIO1 and OPHIO2, DNA transposons of the Dutch elm disease fungi

(2007) Guillaume F. Bouvet et al.   FUNGAL GENETICS AND BIOLOGY