ArticlePloS one2011
LTR retrotransposons in fungi.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Article
- Chromosome-scale genome assembly and characterization of Saccharomycopsis schoenii, a necrotrophic predatory yeast.G3 (Bethesda, Md.) · 2026Article
- Article
- The dynamics of transposable element content in the genome of the human pathogen Histoplasma.Fungal genetics and biology : FG & B · 2026Article
- High-quality genome assembly and comparative analysis reveal extensive genomic variation inMicrobial genomics · 2025Article
- A near-complete telomere-to-telomere genome assembly for Batrachochytrium dendrobatidis GPL JEL423 reveals a larger CBM18 gene family and a smaller M36 metalloprotease gene family than previously recognized.G3 (Bethesda, Md.) · 2025Article
- Volcano: a pipeline to characterize long terminal repeat-retrotransposons families in plants.Bioinformatics advances · 2025Article
- 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.G3 (Bethesda, Md.) · 2024Article
- What are the 100 most cited fungal genera?Studies in mycology · 2024Article
- Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment ineLife · 2024Article
- The Comparative Genomics of Botryosphaeriaceae Suggests Gene Families ofJournal of fungi (Basel, Switzerland) · 2024Article
- The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut.BMC genomics · 2024Article
- From tradition to innovation: conventional and deep learning frameworks in genome annotation.Briefings in bioinformatics · 2024Review
- Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment inbioRxiv : the preprint server for biology · 2024Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Article
- Genetic diversity and population structure of Saccharomyces cerevisiae isolated from Turkish sourdough by iPBS-retrotransposons markers.Archives of microbiology · 2022Article
- In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi.Journal of fungi (Basel, Switzerland) · 2022Article
- Tracking of Diversity and Evolution in the Brown Rot FungiFrontiers in microbiology · 2022Article
- Beneficial bacterial-Frontiers in microbiology · 2022Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (<50 elements), others demonstrate huge expansions (>8000 elements). The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other.
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