The production and quality of apricots in China is currently limited by the availability of germplasm resource characterizations, including identification at the species and cultivar level. To help address this issue, the complete chloroplast genomes of Prunus armeniaca L., P. sibirica L. and kernel consumption apricot were sequenced, characterized, and phylogenetically analyzed. The three chloroplast (cp) genomes ranged from 157,951 to 158,224 bp, and 131 genes were identified, including 86 protein-coding genes, 37 rRNAs, and 8 tRNAs. The GC content ranged from 36.70% to 36.75%. Of the 170 repetitive sequences detected, 42 were shared by all three species, and 53–57 simple sequence repeats were detected with AT base preferences. Comparative genomic analysis revealed high similarity in overall structure and gene content as well as seven variation hotspot regions, including psbA-trnK-UUU, rpoC1-rpoB, rpl32-trnL-UAG, trnK-rps16, ndhG-ndhI, ccsA-ndhD, and ndhF-trnL. Phylogenetic analysis showed that the three apricot species clustered into one group, and the genetic relationship between P. armeniaca and kernel consumption apricot was the closest. The results of this study provide a theoretical basis for further research on the genetic diversity of apricots and the development and utilization of molecular markers for the genetic engineering and breeding of apricots.

Prunus sibirica L. is a key ecological and economic tree species in northern China that is threatened by habitat degradation due to climate change and human activities. To address the gaps of incomplete historical dynamics and lack of conservation integration in existing studies, we integrated MaxEnt and Zonation v4.0 to predict its suitable habitat across five periods (LIG to 2090s) and three CMIP6 SSP scenarios, identifying key drivers and priority conservation zones. The model showed high prediction accuracy (mean AUC > 0.9). Results indicated that Human Footprint (HFP), Precipitation Seasonality (Bio15), Annual Mean Temperature (Bio1), Elevation (ELEV), and Mean Temperature of the Coldest Quarter (Bio11) were the key environmental factors (cumulative contribution 91.4%), with Bio1, Bio15, Temperature Seasonality (Bio4), and HFP confirmed as major drivers (AUC > 0.8) via jackknife test. Spatiotemporally, the species’ suitable habitat contracted from the Last Interglacial to the Last Glacial Maximum and expanded to the current total suitable area of 506,620.1 km². Under future SSP scenarios, suitable habitats expanded continuously under SSP126 and SSP245 but showed a “first expansion then contraction” trend under SSP585, with a persistent northeastward migration of the habitat centroid. The vertical (altitudinal) distribution of P. sibirica showed a trend of moving to higher elevations under future warming scenarios, especially in the SSP585 scenario. High-priority conservation zones are concentrated in northern China with insufficient existing protection. It is emphasized that this study contributes to improving the adaptive capacity and genetic characterization of P. sibirica almond populations to future climate.