The chromosome-level genome assembly of Dryopteris fragrans reveals transposon-mediated genome evolution

Ferns are ancient vascular plants pivotal to plant evolution research, yet genomic resources for specialist-habitat species remain scarce. Here, we present a high-quality chromosome-level genome assembly of Dryopteris fragrans, belonging to a basal lineage of Dryopteridaceae, and investigate its genomic evolution drivers via comparative genomics analysis. No recent whole-genome duplication was detected in D. fragrans; instead, transposable elements, the major genomic component, were identified as the primary evolutionary driver, associated with stress-responsive gene family expansion. Specifically, transposable elements shape gene structure by driving intron expansion (e.g., terpene synthase genes) and forming long-intron genes; transposable elements insertions in promoters also correlate with altered gene expression and increased alternative splicing. This study assembled a high-quality genome of a fern from Dryopteridaceae, and reveals that transposable elements may serve as potential key drivers of D. fragrans genomic evolution. Our findings advance understanding of transposable elements functions in non-seed plants. A chromosome-level genome assembly is generated for the fern Dryopteris fragrans. The findings reveal that transposon insertions have profoundly shaped gene structure and expression, highlighting their role in driving genome evolution