ArticleGenome biology and evolution2009
Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.
Article in Genome biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed, 127 citations in OpenAlex.
- TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.PLoS computational biology · 2026Article
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- Terrier: a deep learning repeat classifier.Briefings in bioinformatics · 2025Article
- Transposable Elements Drive Regulatory and Functional Innovation of F-box Genes.Molecular biology and evolution · 2025Article
- Loss-of-function mutations in the fruit softening geneHorticulture research · 2025Article
- High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.Genome biology and evolution · 2024Article
- Genome-wide survey of the bipartite structure and pathogenesis-related genes ofFrontiers in microbiology · 2024Article
- The good, the bad and the ugly of transposable elements annotation tools.Genetics and molecular biology · 2024Article
- Maternal dominance contributes to subgenome differentiation in allopolyploid fishes.Nature communications · 2023Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes.Frontiers in plant science · 2023Article
- Identification of Daboia siamensis venome using integrated multi-omics data.Scientific reports · 2022Article
- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
- Development of molecular markers based on LTR retrotransposon in the Cleistogenes songorica genome.Journal of applied genetics · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Dfam community resource of transposable element families, sequence models, and genome annotations.Mobile DNA · 2021Article
- Computational Analysis of Transposable Elements and CircRNAs in Plants.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- RepeatModeler2 for automated genomic discovery of transposable element families.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Genome of 'Charleston Gray', the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection.Plant biotechnology journal · 2019Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE sequences. Using control repeat libraries, we show that the program can classify accurately virtually any known TE types. Combining REPCLASS to ab initio repeat finding in the genomes of Caenorhabditis elegans and Drosophila melanogaster allowed us to recover the contrasting TE landscape characteristic of these species. Unexpectedly, REPCLASS also uncovered several novel TE families in both genomes, augmenting the TE repertoire of these model species. When applied to the genomes of distant Caenorhabditis and Drosophila species, the approach revealed a remarkable conservation of TE composition profile within each genus, despite substantial interspecific covariations in genome size and in the number of TEs and TE families. Lastly, we applied REPCLASS to analyze 10 fungal genomes from a wide taxonomic range, most of which have not been analyzed for TE content previously. The results showed that TE diversity varies widely across the fungi "kingdom" and appears to positively correlate with genome size, in particular for DNA transposons. Together, these data validate REPCLASS as a powerful tool to explore the repetitive DNA landscapes of eukaryotes and to shed light onto the evolutionary forces shaping TE diversity and genome architecture.
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