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

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Sex or no sex: Evolutionary adaptation occurs regardless

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Subtelomeres as Specialized Chromatin Domains

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The genomic determinants of adaptive evolution in a fungal pathogen

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Predicting Secretory Proteins with SignalP

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Analysis of RNA-Seq Data Using TEtranscripts

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Data Analysis

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

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Degenerate MAGGY elements in a subgroup of Pyricularia grisea: a possible example of successful capture of a genetic invader by a fungal genome

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Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

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

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Pan-Genome of Wild and Cultivated Soybeans

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

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

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

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

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How retrotransposons shape genome regulation

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LTR-retrotransposons in plants: Engines of evolution

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

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Retrotransposon Tf1 Is Targeted to Pol II Promoters by Transcription Activators

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Filamentous pathogen effector functions: of pathogens, hosts and microbiomes

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

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Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes

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RIP: the evolutionary cost of genome defense

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

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Transposable Elements Direct The Coevolution between Plants and Microbes

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Stronger When Together: Clustering of Plant NLR Disease resistance Genes

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

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Genome evolution: Sex and the transposable element

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

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A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

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The methylated component of the Neurospora crassa genome

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The role of RNA interference in heterochromatic silencing

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Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

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Bursts of retrotransposition reproduced in Arabidopsis

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

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A chromosome conformation capture ordered sequence of the barley genome

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Improved maize reference genome with single-molecule technologies

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

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

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

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Fast gapped-read alignment with Bowtie 2

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

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The evolutionary dynamics of eukaryotic gene order

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Transposable elements and the epigenetic regulation of the genome

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A unified classification system for eukaryotic transposable elements

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Transposable elements and the evolution of regulatory networks

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Mechanisms of change in gene copy number

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Erratum: Evolution and genome architecture in fungal plant pathogens

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Evolution and genome architecture in fungal plant pathogens

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

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Diversity of cytosine methylation across the fungal tree of life

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Computational tools to unmask transposable elements

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Multiple wheat genomes reveal global variation in modern breeding

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Transposable elements contribute to fungal genes and impact fungal lifestyle

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Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution

inferredcites →https://doi.org/10.1073/pnas.0705238104openalex-snapshot

Long-term evolution of transposable elements

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

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Fate of a mutation in a fluctuating environment

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

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The origin and behavior of mutable loci in maize

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Mutation as a Stress Response and the Regulation of Evolvability

inferredcites →https://doi.org/10.1093/bioinformatics/btp248openalex-snapshot

CROC: finding chromosomal clusters in eukaryotic genomes

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

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

inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot

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

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

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

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

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circlize implements and enhances circular visualization in R

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

inferredcites →https://doi.org/10.1093/bioinformatics/btv562openalex-snapshot

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

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

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

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Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses

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Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion

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Causes and Consequences of Genome Expansion in Fungi

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

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

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Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots

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The Origins of Genome Architecture

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Chromosome Rearrangements and the Evolution of Genome Structuring and Adaptability

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A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA

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

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

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Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen

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

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Transposon integration enhances expression of stress response genes

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

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

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

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Variances of the average numbers of nucleotide substitutions within and between populations.

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

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

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

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Contribution of unfixed transposable element insertions to human regulatory variation

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

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A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

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Whole genome comparisons of ergot fungi reveals the divergence and evolution of species within the genus Claviceps are the result of varying mechanisms driving genome evolution and host range expansion

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Subtelomeric regions and a repeat-rich chromosome harbor multicopy effector gene clusters with variable conservation in multiple plant pathogenic Colletotrichum species

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Centromere evolution in the fungal genus Verticillium

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The multi-speed genome of Fusarium oxysporum reveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events

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Verticillium dahliae strains that infect the same host plant display highly divergent effector catalogs

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In planta chromatin immunoprecipitation in Zymoseptoria tritici reveals chromatin-based regulation of putative effector gene expression

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

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

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Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

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

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Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

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Structural variants in 3000 rice genomes

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Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis

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An Overview of Gibberellin Metabolism Enzyme Genes and Their Related Mutants in Rice

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Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice

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

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

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Telomeres and a repeat‐rich chromosome encode effector gene clusters in plant pathogenic Colletotrichum fungi

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

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PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION

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Physiology and molecular aspects of Verticillium wilt diseases caused by V. dahliae and V. albo‐atrum

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The impact of transposable elements in adaptive evolution

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

inferredcites →https://doi.org/10.1111/mpp.12520openalex-snapshot

Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts

inferredcites →https://doi.org/10.1111/mpp.12682openalex-snapshot

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

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The need for speed: compartmentalized genome evolution in filamentous phytopathogens

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Origin and evolution of the plant immune system

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

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Structural Dynamics of Eukaryotic Chromosome Evolution

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The Origins of Genome Complexity

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The B73 Maize Genome: Complexity, Diversity, and Dynamics

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Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

inferredcites →https://doi.org/10.1126/science.1193070openalex-snapshot

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

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Repeat-induced G-C to A-T Mutations in Neurospora

inferredcites →https://doi.org/10.1126/science.aad5497openalex-snapshot

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

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Recurrent evolution of vertebrate transcription factors by transposase capture

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

inferredcites →https://doi.org/10.1128/mbio.00936-15openalex-snapshot

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

inferredcites →https://doi.org/10.1128/mbio.01231-16openalex-snapshot

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

inferredcites →https://doi.org/10.1128/mbio.01714-20openalex-snapshot

Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium

inferredcites →https://doi.org/10.1146/annurev-arplant-050213-035811openalex-snapshot

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

inferredcites →https://doi.org/10.1146/annurev-genet-110711-155616openalex-snapshot

Active Transposition in Genomes

inferredcites →https://doi.org/10.1146/annurev-genom-082410-101412openalex-snapshot

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

inferredcites →https://doi.org/10.1146/annurev-phyto-080508-081748openalex-snapshot

Diversity, Pathogenicity, and Management of Verticillium Species

inferredcites →https://doi.org/10.1146/annurev-phyto-080516-035303openalex-snapshot

The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens

inferredcites →https://doi.org/10.1146/annurev-phyto-080614-120114openalex-snapshot

Understanding Plant Immunity as a Surveillance System to Detect Invasion

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Between a chicken and a grape: estimating the number of human genes

inferredcites →https://doi.org/10.1186/1471-2105-9-18openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1471-2148-7-72openalex-snapshot

Chromatin structure and evolution in the human genome

inferredcites →https://doi.org/10.1186/1471-2164-13-314openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1471-2164-15-891openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1745-6150-4-42openalex-snapshot

Is evolution Darwinian or/and Lamarckian?

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The struggle for life of the genome's selfish architects

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

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

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CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

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LUMPY: a probabilistic framework for structural variant discovery

inferredcites →https://doi.org/10.1186/preaccept-1025065114129803openalex-snapshot

Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content

inferredcites →https://doi.org/10.1186/s12864-015-1347-1openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s12864-016-2690-6openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s12864-017-3795-2openalex-snapshot

Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi

inferredcites →https://doi.org/10.1186/s12864-018-4750-6openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s12915-017-0457-4openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s12915-018-0543-2openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s12915-020-0744-3openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s13059-018-1577-zopenalex-snapshot

Ten things you should know about transposable elements

inferredcites →https://doi.org/10.1186/s13059-020-02060-wopenalex-snapshot

Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life

inferredcites →https://doi.org/10.1186/s13072-015-0033-5openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s13100-020-00215-xopenalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pcbi.1004572openalex-snapshot

Wham: Identifying Structural Variants of Biological Consequence

inferredcites →https://doi.org/10.1371/journal.pgen.1002089openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1006108openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1007467openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1008093openalex-snapshot

Destabilization of chromosome structure by histone H3 lysine 27 methylation

inferredcites →https://doi.org/10.1371/journal.pgen.1008872openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1009448openalex-snapshot

Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen

inferredcites →https://doi.org/10.1371/journal.pone.0029425openalex-snapshot

LTR Retrotransposons in Fungi

inferredcites →https://doi.org/10.1371/journal.pone.0091929openalex-snapshot

PASTEC: An Automatic Transposable Element Classification Tool

inferredcites →https://doi.org/10.1371/journal.ppat.1002137openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.ppat.1002608openalex-snapshot

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

inferredcites →https://doi.org/10.1371/journal.ppat.1003089openalex-snapshot

Loss and Retention of RNA Interference in Fungi and Parasites

inferredcites →https://doi.org/10.1371/journal.ppat.1005920openalex-snapshot

Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens

inferredcites →https://doi.org/10.1534/g3.112.002881openalex-snapshot

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

inferredcites →https://doi.org/10.18637/jss.v025.i01openalex-snapshot

FactoMineR : An R Package for Multivariate Analysis

inferredcites →https://doi.org/10.21775/cimb.004.065openalex-snapshot

Transposable Elements and the Evolution of Eukaryotic Complexity

inferredcites →https://doi.org/10.3389/fpls.2017.00140openalex-snapshot

Characterization of the Two-Speed Subgenomes of Fusarium graminearum Reveals the Fast-Speed Subgenome Specialized for Adaption and Infection

inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot

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

inferredcites →https://doi.org/10.5860/choice.45-0862openalex-snapshot

The origins of genome architecture

inferredcites →https://doi.org/10.7554/elife.20777openalex-snapshot

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

inferredcites →https://doi.org/10.7554/elife.25762openalex-snapshot

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution

inferredcites →https://doi.org/10.7554/elife.62208openalex-snapshot

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

inferredcites →https://doi.org/10.7554/elife.69249openalex-snapshot

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

inferredcites →https://doi.org/10.7717/peerj.7447openalex-snapshot

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

inferredcites →https://doi.org/10.7717/peerj.8214openalex-snapshot

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

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Haplotype-resolved genomes of Phlebopus portentosus reveal nuclear differentiation, TE-mediated variation, and saprotrophic potential

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General Trends of Genomic Signatures of the Ectomycorrhizal Symbiosis in Fungi: A Comparison Across Multiple Lineages

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Integrated Omics Approaches to Accelerate New Strategies for Crop Improvement

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Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation

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Extensive horizontal transfer of transposable elements shapes fungal mobilomes

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The dynamics of transposable element content in the genome of the human pathogen Histoplasma

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Comparative genomics of Cadophora luteo-olivacea reveals a divergent lineage, conserved functional repertoires, and strain-level phenotypic variation

inferred← citeshttps://doi.org/10.1016/j.tig.2021.08.005openalex-snapshot

A devil's bargain with transposable elements in plant pathogens

inferred← citeshttps://doi.org/10.1016/j.tig.2024.08.006openalex-snapshot

Starships: a new frontier for fungal biology

inferred← citeshttps://doi.org/10.1016/j.tplants.2022.06.011openalex-snapshot

Genetic co-option into plant–filamentous pathogen interactions

inferred← citeshttps://doi.org/10.1038/s41467-023-37551-4openalex-snapshot

Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

inferred← citeshttps://doi.org/10.1038/s41467-024-45884-xopenalex-snapshot

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inferred← citeshttps://doi.org/10.1038/s41467-025-61986-6openalex-snapshot

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution

inferred← citeshttps://doi.org/10.1038/s41467-025-62213-yopenalex-snapshot

Transposons and accessory genes drive adaptation in a clonally evolving fungal pathogen

inferred← citeshttps://doi.org/10.1038/s41598-025-05414-1openalex-snapshot

Independent evolution of betulin biosynthesis in Inonotus obliquus

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Warm temperatures inhibit disease progression of Verticillium nonalfalfae in Ailanthus altissima , regardless of virulence

inferred← citeshttps://doi.org/10.1093/g3journal/jkae055openalex-snapshot

Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis

inferred← citeshttps://doi.org/10.1093/g3journal/jkae194openalex-snapshot

Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii

inferred← citeshttps://doi.org/10.1093/g3journal/jkag214openalex-snapshot

A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy

inferred← citeshttps://doi.org/10.1093/gbe/evac165openalex-snapshot

Highlight: Virtual Issue on Host–Pathogen Interactions and Antimicrobial Drug Resistance

inferred← citeshttps://doi.org/10.1093/gbe/evad036openalex-snapshot

Effects ofWolbachiaon Transposable Element Expression Vary BetweenDrosophila melanogasterHost Genotypes

inferred← citeshttps://doi.org/10.1093/gbe/evae272openalex-snapshot

Investigating the Impact of Whole-Genome Duplication on Transposable Element Evolution in Teleost Fishes

inferred← citeshttps://doi.org/10.1093/pnasnexus/pgag254openalex-snapshot

Intermittent fasting rewires tissue-specific gene–transposable element regulatory networks

inferred← citeshttps://doi.org/10.1094/mpmi-06-22-0138-ropenalex-snapshot

Pathogenicity Variation in Two Genomes of Cercospora Species Causing Gray Leaf Spot in Maize

inferred← citeshttps://doi.org/10.1094/mpmi-09-24-0115-fiopenalex-snapshot

From Lesions to Lessons: Two Decades of Filamentous Plant Pathogen Genomics

inferred← citeshttps://doi.org/10.1099/mgen.0.001326openalex-snapshot

Population-level whole-genome sequencing of Ascochyta rabiei identifies genomic loci associated with isolate aggressiveness

inferred← citeshttps://doi.org/10.1101/2022.06.13.495685openalex-snapshot

The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes

inferred← citeshttps://doi.org/10.1101/2022.11.22.517554openalex-snapshot

A single Verticillium dahliae effector determines pathogenicity on tomato by targeting auxin response factors

inferred← citeshttps://doi.org/10.1101/2023.04.04.535574openalex-snapshot

Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen

inferred← citeshttps://doi.org/10.1101/2023.10.17.562820openalex-snapshot

Universal signatures of transposable element compartmentalization across eukaryotic genomes

inferred← citeshttps://doi.org/10.1101/2023.12.22.572151openalex-snapshot

Investigating the impact of whole genome duplication on transposable element evolution in ray-finned fishes

inferred← citeshttps://doi.org/10.1101/2024.05.30.596583openalex-snapshot

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

inferred← citeshttps://doi.org/10.1101/2025.01.08.631984openalex-snapshot

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution

inferred← citeshttps://doi.org/10.1101/2025.01.26.634911openalex-snapshot

The dominant lineage of Phakopsora pachyrhizi in the United States of America does not have a Brazilian origin

inferred← citeshttps://doi.org/10.1101/2025.04.10.648237openalex-snapshot

Transposable elements facilitate the unintentional domestication of a cheese-associated Penicillium mold

inferred← citeshttps://doi.org/10.1101/2025.08.27.672719openalex-snapshot

Genome compartmentalization in a host-specific fungal insect pathogen reveals a putative mating type locus on an accessory chromosome

inferred← citeshttps://doi.org/10.1111/mpp.70039openalex-snapshot

Comparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini

inferred← citeshttps://doi.org/10.1111/mpp.70135openalex-snapshot

Population Genomics Reveals Distinct Lineage of the Asian Soybean Rust Fungus Phakopsora pachyrhizi in the United States of America Unrelated to Brazilian Populations

inferred← citeshttps://doi.org/10.1111/nph.17907openalex-snapshot

Using structural variants to understand the ecological and evolutionary dynamics of fungal plant pathogens

inferred← citeshttps://doi.org/10.1111/nph.18576openalex-snapshot

A highly polymorphic effector protein promotes fungal virulence through suppression of plant‐associated Actinobacteria

inferred← citeshttps://doi.org/10.1111/nph.19604openalex-snapshot

Segmental duplications drive the evolution of accessory regions in a major crop pathogen

inferred← citeshttps://doi.org/10.1111/nph.70686openalex-snapshot

Undermining the cry for help: the phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria

inferred← citeshttps://doi.org/10.1111/nph.71314openalex-snapshot

Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry

inferred← citeshttps://doi.org/10.1128/mbio.02840-23openalex-snapshot

Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen

inferred← citeshttps://doi.org/10.1186/s12915-024-01818-zopenalex-snapshot

Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes

inferred← citeshttps://doi.org/10.1186/s13059-025-03742-zopenalex-snapshot

Characterization of the transposable element landscape shaping the Ectocarpus genome

inferred← citeshttps://doi.org/10.1186/s13100-024-00312-1openalex-snapshot

A systematic screen for co-option of transposable elements across the fungal kingdom

inferred← citeshttps://doi.org/10.1371/journal.pgen.1010804openalex-snapshot

The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods

inferred← citeshttps://doi.org/10.1371/journal.pgen.1011452openalex-snapshot

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

inferred← citeshttps://doi.org/10.1371/journal.ppat.1011525openalex-snapshot

Epigenetic regulation of nuclear processes in fungal plant pathogens

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1463779openalex-snapshot

Genomic insights into Verticillium: a review of progress in the genomics era

inferred← citeshttps://doi.org/10.3389/fpls.2022.811152openalex-snapshot

Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence

inferred← citeshttps://doi.org/10.3390/ijms222111387openalex-snapshot

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

inferred← citeshttps://doi.org/10.3390/jof10090632openalex-snapshot

Comparative Genomics of Fungi in Nectriaceae Reveals Their Environmental Adaptation and Conservation Strategies

inferred← citeshttps://doi.org/10.3390/jof8121238openalex-snapshot

Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae

inferred← citeshttps://doi.org/10.3390/pharmaceutics14091837openalex-snapshot

How to Completely Squeeze a Fungus—Advanced Genome Mining Tools for Novel Bioactive Substances

inferred← citeshttps://doi.org/10.6084/m9.figshare.26670309openalex-snapshot

Additional file 1 of A systematic screen for co-option of transposable elements across the fungal kingdom

inferred← citeshttps://doi.org/10.6084/m9.figshare.26670312openalex-snapshot

Additional file 2 of A systematic screen for co-option of transposable elements across the fungal kingdom

inferred← citeshttps://doi.org/10.6084/m9.figshare.26670315openalex-snapshot

Additional file 3 of A systematic screen for co-option of transposable elements across the fungal kingdom

inferred← citeshttps://doi.org/10.64898/2026.04.07.716880openalex-snapshot

Comparative genomics of Cadophora luteo-olivacea reveals a divergent lineage, conserved functional repertoires, and strain-level variation in pathogenicity

inferred← citeshttps://doi.org/10.64898/2026.09.23.753852openalex-snapshot

Graph-based pangenome of Venturia inaequalis, the apple scab fungus, reveals structural variants associated with population differentiation

inferred← citeshttps://doi.org/10.64898/2026.10.01.755987openalex-snapshot

Genome-wide structural variants uncover strain-specific genes and evolutionary genomic determinants of a fungal maize pathogen

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