BryoCAD: Extending Plant DNA Foundation Models Beyond Flowering Plants

BryoCAD, a bryophyte-adapted DNA language model, raises mean zero-shot motif-recovery accuracy from 45.7% to 57.0% on three bryophyte genomes, outperforming PlantCAD2-Small.

• Why it matters: Functional interpretation in bryophytes is limited by incomplete annotations and scarce experiments, and it is unclear whether DNA foundation models transfer to evolutionarily divergent lineages.
• What they did: BryoCAD was built by continued pre-training of the angiosperm-specific PlantCAD2 on 17 bryophyte genomes, then evaluated on four gene-boundary motif recovery tasks and gene-structure annotation.
• The result: BryoCAD-Small improved transcript-level F1 scores for Marchantia polymorpha (0.578→0.625) and Physcomitrium patens (0.485→0.530), supporting lineage-specific adaptation for bryophyte sequence interpretation.

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