Genetic diversity and population differentiation of Parrotia subaequalis revealed by RAD-seq

<i>Parrotia subaequalis</i> (H. T. Chang) R.M. Hao & H.T. Wei is an endemic species of China that occupies an important phylogenetic position within the family Hamamelidaceae. To systematically evaluate its genetic diversity and population genetic structure, we conducted reduced-representation genome resequencing of 233 individuals from nine natural populations. In addition, Oxford Nanopore Technologies (ONT) long-read sequencing data and raw Hi-C data released in the NCBI public database were used to perform <i>de novo</i> genome assembly and chromosome-level scaffolding, generating a reference genome for population genetic analyses. A total of 2,716,976 SNPs were detected, and after quality control and filtering, 136,252 high-quality SNPs were retained for subsequent analyses. Genetic diversity analyses showed that the mean number of alleles (Na) across populations was 1.83, the effective number of alleles (Ne) was 1.24, the polymorphism information content (PIC) was 0.146, and nucleotide diversity (Pi) was 0.000037. The overall observed heterozygosity (Ho) and expected heterozygosity (He) were 0.092 and 0.170, respectively, indicating a moderately low level of genetic diversity in this species. Principal component analysis (PCA), population structure inference, and phylogenetic reconstruction based on SNP data consistently supported a distinct three-cluster genetic structure: the Taoling (TL) population formed a relatively independent genetic lineage; the Longchishan (LCS) and Gujingyuan (SDG) populations showed genetic proximity with partial overlap; and the remaining six populations clustered into another group. Pairwise <i>F</i> _st values among populations ranged from 0.0168 to 0.1082, indicating weak to moderate genetic differentiation among populations, with the highest differentiation observed between the TL population and the others. Linkage disequilibrium (LD) decay rates differed among populations, with slower LD decay in the LWS population, potentially associated with changes in its effective population size (Ne). Overall, this study revealed the geographic genetic structure and spatially restricted gene flow of <i>P. subaequalis</i>, providing important genetic evidence for defining conservation units and formulating <i>in situ</i> and <i>ex situ</i> conservation strategies, as well as for the preservation and utilization of germplasm resources.