As the wild progenitor population of cultivated apricots, Xinjiang wild apricots hold irreplaceable significance in maintaining ecosystem functions and conserving germplasm resources. This study employed a combined approach utilising chloroplast DNA fragments (rpl32-trnL and ndhC-trnV) and a single-copy nuclear gene (DXH) to conduct a systematic phylogeographic analysis of wild apricot resources within the Ili wild fruit forests of Xinjiang. Results indicate significant divergence between genetic structures revealed by chloroplast DNA and nuclear genes, reflecting complex evolutionary processes driven by natural selection, genetic drift, and gene flow across distinct genetic systems. Genetic variation predominantly resided within populations, with weak differentiation between them. Neutrality tests and mismatch analysis indicated that wild apricot maternal lineages had not undergone significant historical expansions, suggesting a possible shared population contraction (bottleneck effect). Conversely, nuclear gene data supported recent expansion, with the Yining County population exhibiting the most pronounced expansion signal, indicating effective recording of this event by the nuclear genome. Niche modelling using the MaxEnt approach indicates that key environmental factors influencing wild apricot distribution include precipitation during the wettest season (100~135 mm), precipitation during the warmest season (90~120 mm), and soil sand content (6%~38%). The current suitable habitat is primarily concentrated in the Ili Kazakh Autonomous Prefecture, while projections under future climate scenarios indicate an expansion trend in its suitable range. This study systematically elucidates the genetic diversity characteristics and phylogeographic patterns of Xinjiang wild apricot, clarifying its population history dynamics and future distribution potential. It provides theoretical foundations and practical guidance for the scientific conservation and sustainable utilisation of germplasm resources for this species.

Background: The phylogenetic placement and chloroplast-inferred maternal relationships of commercial pluot cultivars remain unclear, largely because plastome-level evidence is limited for assessing their affinities with Prunus salicina and Prunus ussuriensis. Although chloroplast genome structure has been well characterized in angiosperms and in several Prunus species, complete plastome resources and comparative genomic evidence for commercial pluot cultivars remain scarce. Methods: Here, we assembled the complete chloroplast genomes of six commercial pluot cultivars and performed comparative genomic, phylogenomic, and divergence time analyses using representative Prunus species. Results: All genomes exhibited the typical circular quadripartite structure and ranged from 157,865 to 158,138 bp in length. Genome organization, GC content, and gene content were highly conserved, whereas the IR regions showed an elevated GC content of approximately 42.6%, owing to rRNA gene enrichment. IR boundary comparison revealed contraction at the IRb/SSC boundary in P. ussuriensis, while pluot cultivars were structurally more similar to P. salicina. In total, 370 SSR loci and four hypervariable regions, namely rpoB–trnC-GCA, petN–psbM, trnV-UAC–trnM-CAU, and trnP-UGG–psaJ, were identified as candidate molecular markers for Prunus germplasm identification and genetic analysis. Phylogenomic analysis resolved four major clades within Prunus and showed that ‘Flavor King’, ‘Flavor Supreme’, and ‘Flavor Queen’ grouped with P. ussuriensis, whereas ‘Flavorosa’, ‘Dinosaur Egg’, and ‘Flavorich’ grouped with P. salicina. Conclusion: Overall, this study provides the first comparative plastome analysis of six commercial pluot cultivars and offers chloroplast-level evidence for their maternal affinities within Prunus, together with useful marker resources for cultivar identification and germplasm evaluation.