ArticleBMC genomics2026
EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis.
Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
1 citing paper in PubMed.
- Haplotype-resolved genome of Citrus × sinensis 'Pera IAC', the most widely cultivated sweet orange in Brazil.Scientific data · 2026Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundTransposable elements (TEs) are major components of plant genomes, shaping genome architecture, gene regulation, and evolutionary innovation. While the Extensive de novo TE Annotator (EDTA) pipeline remains one of the most accurate and widely adopted tools for TE annotation, its command-line interface constrains accessibility, and the current parameterization is suboptimal for non-model plant species. Lineage-level classification and detailed annotation of non-autonomous elements are often missing in existing pipelines, both of which are essential for accurate interpretation of plant TE landscapes.
resultsEDTA-GUI was developed as a graphical implementation of the EDTA pipeline, preserving its validated annotation accuracy while introducing plant-optimized parameterization. This mode incorporates genome-size-aware adjustments, domain-based filtering, lineage-level classification, refined subtyping of LTR retrotransposons, and enhanced detection of non-autonomous elements. An integrated visualization suite generates publication-ready figures and summary reports, facilitating interpretability and reproducibility. Benchmarking across 12 representative plant and algal genomes demonstrates that EDTA-GUI retains the sensitivity, specificity, and F1-scores of the original EDTA pipeline, while enabling fine-grained classification and improved biological interpretability. Using EDTA-GUI, we annotated 75 plant, algal, and microalgal genomes and created the freely available AnnoTEP-DB (Annotation of Transposable Elements in Plants Database) repository, allowing users to browse, visualize, and download TE libraries, classification summaries, GFF3 annotations, soft-masked genomes, and graphical summaries.
conclusionEDTA-GUI provides a unified and accessible framework for comprehensive TE annotation across the plant tree of life. By integrating lineage-aware classification, accurate identification of non-autonomous derivatives, and automated visualization, the pipeline produces biologically meaningful TE catalogs suitable for integrative genomic, epigenomic, and evolutionary analyses. Together with AnnoTEP-DB, this resource enhances reproducibility, transparency, and accessibility in plant genomics, supporting large-scale comparative and evolutionary studies of TE-mediated regulatory innovation.
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Registered trials
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.