GeneCAD: Plant Genome Annotation with a DNA Foundation Model.

ABSTRACT: Accurate genome annotation remains a bottleneck in plants, where polyploidy and repeat-rich sequence confound homology- and RNA-based pipelines. We introduce GeneCAD, a sequence-only method that predicts complete plant gene models directly from DNA. GeneCAD couples representations from a plant DNA foundation model, PlantCAD2, with a lightweight ModernBERT encoder and a chromosome-wide conditional random field that enforces splice-phase and feature order, and applies a protein language-model screen to suppress repeat-driven open reading frames. To limit label noise, we rank and filter public annotations using a sequence-based masked-motif score and fine-tune on five phylogenetically diverse, high-quality references. Across five held out angiosperms, including the allotetraploid Nicotiana

SUBMITTER: Liu ZY 

PROVIDER: S-EPMC12637538 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature