PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants

Résumé fourni par la source

Flowering plants (angiosperms) exhibit extraordinary species diversity, ∼200-fold variation in genome size, and relatively compact coding regions, presenting both a unique challenge and opportunity for DNA language models. Here, we introduce PlantCAD2, an extended-context, plant-specific DNA language model with single-nucleotide resolution, pre-trained on 65 angiosperm genomes, together with a series of public benchmarks for evaluation. Comprehensive zero-shot testing shows that PlantCAD2 (676 million parameters) efficiently captures evolutionary conservation, surpassing the 7-billion-parameter Evo2 in 10 of 12 tasks. With parameter-efficient fine-tuning, PlantCAD2 outperforms the 1-billion-parameter AgroNT across seven cross-species tasks including chromatin accessible region, gene expression, and protein translation. Its 8,192-bp context window substantially improves accessible chromatin prediction in large genomes such as maize (area under the precision-recall curve [AUPRC] increasing from 0.587 to 0.711), underscoring the importance of long-range context for modeling distal regulation. These results establish PlantCAD2 as a powerful and versatile foundation model for plant genome annotation and interpretation across diverse species.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.