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

A population-level chloroplast-genome study of the Mongolian Plateau shrub Prunus mongolica identified four genetic groups that corresponded to distinct geographic regions. Researchers sequenced complete chloroplast genomes from 153 individuals representing 26 populations, then compared population structure, phylogenetic relationships, principal components, and haplotype networks. These approaches consistently supported the four-group pattern.

The study also estimated that P. mongolica diverged from P. davidiana 2.35 million years ago and found four finer-scale clades within the sampled species. The results provide a chloroplast-based view of the shrub’s population structure, genetic diversity, and divergence history, although they do not represent a complete assessment of variation across the plant genome. All 153 chloroplast genomes had a typical quadripartite structure and ranged from 157,767 to 158,164 base pairs in length.

Their mean GC content was 36.74%. Each genome contained 131 genes, comprising 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Seventeen genes were duplicated in the inverted repeats, while 18 genes contained introns.

Simple sequence repeats were concentrated in non-coding regions, and A/T mononucleotide repeats predominated among the 16 simple-sequence-repeat types identified. Palindromic repeats were the most abundant dispersed repeats. The conserved gene content and narrow range of genome lengths contrasted with the variation subsequently detected among individual chloroplast genomes.

Across the complete sample, the researchers identified 713 polymorphic sites, with single-nucleotide variants occurring more frequently than other variant classes. Among coding sequences, ndhF was the most polymorphic gene, and NADH dehydrogenase genes had the highest polymorphism within the functional categories evaluated. The atpF-atpH intergenic spacer was the most variable intergenic region.

Codon-usage analysis showed a strong A/T preference at the third codon position, with the study identifying natural selection as the principal influence on this pattern. Tests for selective pressure did not detect significant episodic positive selection, while generally low background omega values indicated that purifying selection predominated in the chloroplast protein-coding genes examined. Population analyses of the 26 sampled populations resolved four geographic groups.

The fourth group had the highest reported haplotype diversity, with Hd = 0.903 and nucleotide diversity, Pi, of 0.00028. The greatest differentiation occurred between groups 1 and 3, which had an F ST of 0.84125. The same broad division was recovered by phylogenetic reconstruction, principal component analysis, and haplotype-network analysis, providing convergent support for the geographic structure.

Because the evidence came from chloroplast genomes, the findings principally describe the maternal phylogeographic structure of P. mongolica ; the supplied study does not establish whether the same pattern occurs in nuclear DNA or other forms of genetic variation. For the wider evolutionary analysis, the researchers examined 35 chloroplast genomes across Rosaceae. They estimated Rosaceae divergence at 91.98 million years ago, Prunus crown divergence at 7.41 million years ago, and the split between P. mongolica and P. davidiana at 2.35 million years ago.

A high-resolution analysis using all 153 P. mongolica individuals resolved four clades, with reported divergence events at 2.25, 2.23, 2.21, and 2.15 million years ago. These dates are estimates derived from the phylogenetic analyses rather than direct observations of the historical events. Overall, the study documents conserved chloroplast organization alongside substantial variation, pronounced geographic partitioning, and predominantly purifying selection.

It also establishes a population-level genetic baseline for further research on the diversity, biogeography, and conservation of P. mongolica , an ancient relict and endemic shrub whose populations have reportedly declined in size and whose range has contracted as environmental conditions have deteriorated.

Subject of Research: Population-level chloroplast genomics of Prunus mongolica structure, diversity, phylogeny, and divergence history.

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

Article References: Wang, Y., Zhu, Q., Zeng, J., Chen, X., Liang, W., & Zhang, L. (2026). Population-level chloroplast genome insights into population structure, genetic diversity, phylogeny, and divergence time of Prunus mongolica. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10220-6

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10220-6

Keywords: Prunus mongolica, chloroplast genomes, population structure, genetic diversity, phylogeography, Mongolian Plateau, phylogeny, divergence time, purifying selection, plant conservation, Population-level, chloroplast