Decoding the genome of Brainea insignis reveals insights into fern evolution and conservation

Ferns are an ancient lineage of vascular plants, yet limited genomic resources constrain both evolutionary and conservation inference. Here, we generate a chromosome-level genome assembly for the endangered cycad fern Brainea insignis (8.62 Gb), the sole species in its genus within eupolypods II, and integrate comparative and population genomics to resolve its evolutionary history and vulnerability. The genome retains the ancient whole-genome duplication shared by leptosporangiate ferns; however, its exceptional size is driven primarily by recent repeat accumulation and further shaped by lineage-specific evolutionary signatures linked to functional specialization. Resequencing across the range identifies three geographically and environmentally structured lineages shaped by Quaternary refugia, limited postglacial expansion and localized admixture. Recently reduced populations show pronounced genomic erosion, including inbreeding and elevated genetic load, due to insufficient time for purging. We detect climate-associated local adaptation and project substantial future genetic offsets, with southwestern Indochina populations at highest risk. Our results expand fern genomics and support spatially tailored conservation strategies that maintains habitat connectivity and promotes adaptive gene flow.