EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis

Transposable 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. EDTA-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. EDTA-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.