Population-level chloroplast genome insights into population structure, genetic diversity, phylogeny, and divergence time of Prunus mongolica

Prunus mongolica , a deciduous shrub belonging to the genus Prunus of the Rosaceae family, is an endemic and ancient relict plant of the Mongolian Plateau. Its seeds contain 40% edible oil, and its seed kernels have medicinal properties including anti-fibrosis of tissues and organs, anti-tumor, and anti-ulcer inflammation. The ecological environment and worsened the survival conditions of P. mongolica , leading to a sharp decline in population size, a continuous reduction in distribution range, and a certain degree of loss of genetic resource diversity. Therefore, it is very necessary to conduct large-scale chloroplast genome sequencing to analyze the genomic diversity of this ecologically and economically important species. All 153 chloroplast genomes of P. mongolica displayed a typical quadripartite structure, ranging from 157,767 bp to 158,164 bp and mean GC content 36.74%. Each genome contained 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes; 17 genes were duplicated in the IRs, and 18 genes contained introns. Repeat analysis revealed that SSRs were concentrated in non-coding regions, A/T mononucleotide repeats dominated the 16 SSR types, and palindromic repeats were the most abundant dispersed repeats. Across the chloroplast genomes, 713 polymorphic sites were identified, with single-nucleotide variants (SNVs) being the most frequent. Among coding sequences, ndh F was the most polymorphic; NADH dehydrogenase genes showed the highest level of polymorphism among functional categories; and atp F- atp H was the most variable intergenic spacer. Codon usage bias showed a strong A/T preference at the third codon position, with natural selection as the primary shaping factor. Population genetic analyses of 26 populations resolved four groups consistent with phylogenetic, PCA, and haplotype network results; these groups corresponded to distinct geographic regions, with Group 4 showing the highest haplotype diversity (Hd = 0.903; Pi = 0.00028) where Groups 1 and 3 showed the strongest differentiation (Fst = 0.84125). Phylogenetic analysis of 35 chloroplast genomes estimated Rosaceae divergence at 91.98 Mya. Prunus crown divergence at 7.41 Mya, and the split between P. mongolica and P. davidiana at 2.35 Mya. High-resolution analysis of 153 individuals resolved four clades, with divergence events at 2.25, 2.23, 2.21, and 2.15 Ma. Selective pressure analysis detected no significant episodic positive selection, and generally low background ω values indicated predominant purifying selection on chloroplast protein-coding genes. In this study, we conducted a comprehensive and detailed comparative analysis of chloroplast genomes from 153 individuals of P. mongolica , along with phylogenetic reconstruction and divergence time estimation. The results reveal the maternal phylogeographic structure and phytogeographic of P. mongolica . These findings will not only facilitate future research on the genetic diversity and biogeography of this species, but also provide a scientific basis for its conservation.