ArticleNature communications2024
HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Near-complete assembly of wild emmer wheat unveils centromere reorganization during polyploid evolution.Nature genetics · 2026Article
- First chromosome-scale genome of Cornus kousa K2‡.G3 (Bethesda, Md.) · 2026Article
- Evolutionary Consequences of Repeated Loss of Distyly in Linum.Genome biology and evolution · 2026Article
- Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genus-Wide Pan-Genome Analysis ofPlants (Basel, Switzerland) · 2026Article
- Chromosome-Scale Genome of Zoonotic EyewormAnimals : an open access journal from MDPI · 2026Article
- Chromosome-level genome assembly of the Amazonian native fish red-bellied pacu (Piaractus brachypomus).Scientific data · 2026Article
- Pan-Genome Analysis Reveals Evolutionary Dynamics and Functional Divergence of thePlants (Basel, Switzerland) · 2026Article
- Centromeric tandem repeats expansions in plateau zokor enhance chromosome stability for high-altitude adaptation.Genome biology · 2026Article
- Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.Genome biology and evolution · 2026Article
- The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos.The New phytologist · 2026Article
- Complete telomere-to-telomere genomes of cowpea reveal insights into centromere evolution in Phaseoleae.Horticulture research · 2026Article
- Phased potato genome assembly and association genetics enable delineation of the H1 resistance locus against potato cyst nematodes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- Pan-genome-wide characterization of the ascorbate peroxidase gene family reveals evolutionary dynamics and salt-responsive mechanisms in Fraxinus.BMC plant biology · 2026Article
- Near telomere-to-telomere genome assembly of the stone loach (Traccatichthys pulcher).Scientific data · 2026Article
- A chromosome-scale genome assembly of the striped fruit fly Zeugodacus scutellatus (Diptera: Tephritidae).Scientific data · 2026Article
- EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis.BMC genomics · 2026Article
- Pan-NLR gene family analyses decipher evolutionary dynamics, population diversity, and potential disease resistance genes in cucumber.BMC plant biology · 2026Article
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10 authors.
Funding
Abstract
Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, HiTE has identified numerous novel transposons with well-defined structures containing protein-coding domains, some of which are directly inserted within crucial genes, leading to direct alterations in gene expression. A Nextflow version of HiTE is also available, with enhanced parallelism, reproducibility, and portability.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.