ArticlePLoS genetics2016
Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
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Who cites it
126 citing papers in PubMed, 220 citations in OpenAlex.
- 5mC and 6mA DNA Methylation in the Fungal Kingdom: From Genome Defense to Epigenetic Regulation.Epigenomes · 2026Review
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- Genome reshaping by Helitron transposons in Fusarium oxysporum TR4 affects secondary metabolism but not virulence.Nature communications · 2026Article
- Genetic and Epigenetic Mechanisms Underlying Reversible Adaptive Responses in Fungi.Journal of fungi (Basel, Switzerland) · 2026Review
- Interspecies hybridization as a route of accessory chromosome origin in fungal pathogens.mBio · 2026Article
- Establishment of a congenic strain for the oyster mushroom reveals the structure and evolution of mating-type loci.PLoS genetics · 2026Article
- Comparative genome analysis identifies necrosis-inducing effectors in the lentil pathogen Ascochyta lentis in isolates with distinct virulence profiles.BMC genomics · 2026Article
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- The poplar pathogenMicrobial genomics · 2026Article
- Genus-wide comparative genomics ofIMA fungus · 2026Article
- Comparative Transcriptomic Analyses Reveal Potential Stp1 Regulatory Roles Independent of Sre1 inInternational journal of molecular sciences · 2025Article
- FoTeRs: a novel family of telomere-associated retrotransposons in Fusarium oxysporum.Mobile DNA · 2025Article
- High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae.Genome research · 2025Article
- Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom.PLoS biology · 2025Article
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- Patterns and mechanisms of fungal genome plasticity.Current biology : CB · 2025Review
- How genomics can help unravel the evolution of endophytic fungi.World journal of microbiology & biotechnology · 2025Review
- Analyses of Transposable Elements in Arbuscular Mycorrhizal Fungi Support Evolutionary Parallels With Filamentous Plant Pathogens.Genome biology and evolution · 2025Article
- Genomic features of lichen-associated black fungi.IUBMB life · 2025Article
66 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.
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