ArticleGenome research2024
MCHelper automatically curates transposable element libraries across eukaryotic species.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Transposable elements as evolutionary catalysts of ant macrodiversity.Science advances · 2026Article
- The rate and spectrum of germline mutations in chicken from a commercial pedigree line.Genetics, selection, evolution : GSE · 2026Article
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Transposable elements in the era of data science EMBO course: a call for open, accessible, and collaborative TE resources.Mobile DNA · 2026Article
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Ancient Persistence and Newfound Diversity of CR1-Group Retrotransposons Across Vertebrates.Genome biology and evolution · 2026Article
- Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtailbioRxiv : the preprint server for biology · 2026Article
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- Reference genome of an irruptive migrant, the pine siskin (Spinus pinus).The Journal of heredity · 2026Article
- Interspecies hybridization as a route of accessory chromosome origin in fungal pathogens.mBio · 2026Article
- Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species.Genome biology · 2026Article
- Arms races between selfish genetic elements and their host defence in termites.Nature communications · 2026Article
- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
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- Article
- Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements.Genome biology and evolution · 2025Article
- Ancestral and recent bursts of transposition shaped the massive genomes of plant pathogenic rust fungi.BMC genomics · 2025Article
- Horizontal transmission of functionally diverse transposons is a major source of new introns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
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Authors and funding
4 authors.
Funding
Abstract
The number of species with high-quality genome sequences continues to increase, in part due to the scaling up of multiple large-scale biodiversity sequencing projects. While the need to annotate genic sequences in these genomes is widely acknowledged, the parallel need to annotate transposable element (TE) sequences that have been shown to alter genome architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate genome-wide annotation of TE sequences is still technically challenging. Several de novo TE identification tools are now available, but manual curation of the libraries produced by these tools is needed to generate high-quality genome annotations. Manual curation is time-consuming, and thus impractical for large-scale genomic studies, and lacks reproducibility. In this work, we present the Manual Curator Helper tool MCHelper, which automates the TE library curation process. By leveraging MCHelper's fully automated mode with the outputs from three de novo TE identification tools, RepeatModeler2, EDTA, and REPET, in the fruit fly, rice, hooded crow, zebrafish, maize, and human, we show a substantial improvement in the quality of the TE libraries and genome annotations. MCHelper libraries are less redundant, with up to 65% reduction in the number of consensus sequences, have up to 11.4% fewer false positive sequences, and up to ∼48% fewer "unclassified/unknown" TE consensus sequences. Genome-wide TE annotations are also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy-to-install and easy-to-use tool.
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