ArticleMobile DNA2024
Identification of transposable element families from pangenome polymorphisms.
Article in Mobile DNA, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The evolution of structural variation across 500 million years of vertebrate evolution.bioRxiv : the preprint server for biology · 2026Article
- Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtailbioRxiv : the preprint server for biology · 2026Article
- Comparative genomics reveals LINE-1 recombination with diverse RNAs.Cell genomics · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.PLoS computational biology · 2026Article
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Article
- Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals.Genome biology · 2025Article
- FastGA: fast genome alignment.Bioinformatics advances · 2025Article
- Controlling and controlled elements: highlights of the year in mobile DNA research.Mobile DNA · 2024Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundTransposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility.
resultsWe develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies.
conclusionsOur results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.
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