High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region

Despite the ecological importance of karst ecosystems, genomic studies on the conservation and adaptation of karst plant species, particularly threatened wild species, remain scarce. Here, we investigate the genetic architecture, demographic history, and adaptive potential of Oreocharis mileensis , a threatened karst-endemic resurrection plant. We generated a high-quality, phased genome assembly of 3.99 Gb covering two haplotypes with a contig N50 of 124 Mb, revealing three lineage-specific whole-genome duplication events following the ancestral γ event. Population resequencing of 107 individuals across 10 localities uncovered strong population structure, low gene flow, and high genetic differentiation, indicating long-term isolation. Core populations exhibited elevated inbreeding, whereas peripheral populations showed reduced runs of homozygosity and fewer deleterious mutations, suggesting historical demographic events and possible purging effects. pRDA analyses on putatively adaptive loci revealed that genetic variation is primarily aligned with pre-existing population structure. Functional annotation of putatively adaptive SNPs identified genes associated with drought tolerance and rapid recovery after rewatering. Gradient Forest models revealed substantial genomic offset in almost all populations, highlighting their increased vulnerability under projected climate scenarios. Based on these findings, we propose conservation strategies that include delineating eight genetically informed management units and facilitating assisted gene flow among compatible populations. For highly isolated populations, ex situ conservation, habitat restoration, and cultivation for horticultural use are recommended to mitigate genetic erosion and enhance adaptive resilience. This study provides critical insights into how historical, demographic, and environmental factors shape genetic diversity and informs conservation efforts for plant species in fragile karst ecosystems. • A high-quality, phased and haplotype-resolved genome (3.99 Gb for diploid genome; contig N50: 124 Mb) of Oreocharis mileensis reveals three lineage-specific whole-genome duplications post-γ event. • Population genomics of 107 individuals across 10 sites shows strong structure, low gene flow, and high differentiation shaped by population structure, environmental isolation rather than geography. • Core populations exhibit elevated inbreeding, while peripheral populations show signs of possible purging with fewer deleterious mutations and shorter runs of homozygosity. • Adaptive SNPs linked to drought resilience and high predicted genomic offset under climate change inform urgent conservation actions, including eight management units, assisted gene flow, and ex situ strategies.