Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict tree Perkinsiodendron macgregorii.

Relict trees are key to understanding macroevolution, biogeography, and extinction risk under environmental change, yet genome-wide data on diversity and demography remain scarce. Perkinsiodendron macgregorii, a monotypic East Asian relict within Styracaceae, is of notable horticultural and conservation significance. Here, we assembled a chromosome-level genome (∼1.15 Gb) and resequenced 167 individuals from 30 populations across its range. We performed a comparative analysis of single nucleotide polymorphisms (SNPs) and structural variants (SVs) to assess population structure, mutation load, climate-associated variation, and genomic vulnerability. Both SNP and SV datasets consistently resolved two evolutionarily cohesive lineages broadly separated by the Wuyi Mountains. Demographic reconstructions dated East-West divergence to ∼0.16 Ma and revealed a long-term decline in effective population size (N e) since the Late Pleistocene, with lineage-specific fluctuations through the Quaternary. Genome-wide diversity was moderate overall, but the West lineage showed elevated inbreeding and realized genetic load. Relative to SNPs, SVs showed higher proportions of HIGH-impact mutations (i.e., variants more likely to disrupt gene function), consistent with the larger genomic span of SVs and their greater potential deleterious effects. Functional enrichment of core adaptive variants (755 SNPs, 63 SVs) revealed divergent adaptive signals across marker classes. Genomic offset and RONA projections were concordant and highlighted western Jiangxi and southwestern Hunan as future vulnerability hotspots, with risk increasing under higher-emissions scenarios. Together, these results support recognizing East and West lineages as primary conservation units and prioritizing at-risk West populations (JXJGS, HNSHS) for management, while safeguarding genetically distinctive populations (e.g., JXGS, JXYJF) as secondary units to preserve evolutionary potential.