ArticleGenome biology and evolution2012
Patterns of repeat-induced point mutation in transposable elements of basidiomycete fungi.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 71 citations in OpenAlex.
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- How and when organisms edit their own genomes.Nature genetics · 2025Review
- Patterns and mechanisms of fungal genome plasticity.Current biology : CB · 2025Review
- Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi.Nature communications · 2023Article
- Current genetic strategies to investigate gene functions in Trichoderma reesei.Microbial cell factories · 2023Review
- Modulation of C-to-T mutation by recombination-independent pairing of closely positioned DNA repeats.Biophysical journal · 2021Article
- Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation.Genome biology and evolution · 2021Article
- Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements.G3 (Bethesda, Md.) · 2021Article
- Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota.Frontiers in microbiology · 2020Article
- Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements.PloS one · 2020Article
- Repeat-Induced Point Mutations Drive Divergence betweenPathogens (Basel, Switzerland) · 2019Article
- The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations.PeerJ · 2019Article
- Analysis of Repeat Induced Point (RIP) Mutations inGenetics · 2019Article
- Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Genomic and Genetic Insights Into a Cosmopolitan Fungus,Frontiers in microbiology · 2018Article
- Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi.Microbiology spectrum · 2017Review
- Massive Expansion of Gypsy-Like Retrotransposons in Microbotryum Fungi.Genome biology and evolution · 2017Article
- Article
- Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) are ubiquitous genomic parasites that have prompted the evolution of genome defense systems that restrict their activity. Repeat-induced point mutation (RIP) is a homology-dependent genome defense that introduces C-to-T transition mutations in duplicated DNA sequences and is thought to control the proliferation of selfish repetitive DNA. Here, we determine the taxonomic distribution of hypermutation patterns indicative of RIP among basidiomycetes. We quantify C-to-T transition mutations in particular di- and trinucleotide target sites for TE-like sequences from nine fungal genomes. We find evidence of RIP-like patterns of hypermutation at TpCpG trinucleotide sites in repetitive sequences from all species of the Pucciniomycotina subphylum of the Basidiomycota, Microbotryum lychnidis-dioicae, Puccinia graminis, Melampsora laricis-populina, and Rhodotorula graminis. In contrast, we do not find evidence for RIP-like hypermutation in four species of the Agaricomycotina and Ustilaginomycotina subphyla of the Basidiomycota. Our results suggest that a RIP-like process and the specific nucleotide context for mutations are conserved within the Pucciniomycotina subphylum. These findings imply that coevolutionary interactions between TEs and a hypermutating genome defense are stable over long evolutionary timescales.
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