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

Abstract Ferns are ancient vascular plants pivotal to plant evolution research. Although sequencing technologies have advanced fern genomic studies, scarce genomic resources for specialist-habitat ferns limit insights into their genome evolution. Dryopteris fragrans (L.) Schott is a fern endemic to sun-exposed volcanic-lava habitats; here, we generated its high-quality chromosome-level genome assembly, and explored the drivers of its genomic evolution and habitat adaptation via whole-genome duplication (WGD) detection, gene family evolution analysis and other approaches. No recent WGD event was detected in D. fragrans , while transposable elements (TEs)—the major genomic component, associated with the expansion of environment-adaptive gene families—were identified as the primary evolutionary driver. Specifically, TEs shape gene structure by forming clade-specific long-intron genes, regulate gene expression through promoter insertion, and increase alternative splicing events in host genes. This study reports the first high-quality genome of a volcanic-lava-adapted fern, revealing TEs as potential key drivers of D. fragrans ’ genomic evolution and habitat adaptation. Our findings advance understanding of TE functions in non-seed plant evolution, and provide valuable genomic resources for researching early land plant adaptation and regulatory innovation.