LAUSR

Background: Prunus armeniaca, Prunus divaricata, Prunus tianshanica, and Prunus domestica are valuable ancient tree species that have persisted since the end of the Tertiary period within the Tianshan wild fruit forest. However, the evolutionary relationships among Prunus species in the Tianshan wild fruit forest have long posed a challenge. Methods: We sequenced and assembled the chloroplast genomes of P. armeniaca, P. divaricata, and P. tianshanica, and incorporated the chloroplast genome data of P. domestica for comparative analysis to elucidate their phylogenetic positions within the genus Prunus. Results: The lengths of these chloroplast genomes ranged from 157,395 bp to 158,090 bp, with a total of 130 to 131 genes annotated, comprising 85 to 86 protein-coding genes, 8 rRNA genes, and 35 to 36 tRNA genes. Notably, the four wild Prunus species predominantly used high-frequency codons ending in A/U. Additionally, we identified 300 simple repetitive sequences and 166 long repetitive sequences across the four wild Prunus species. The mutation sites were mainly found in the non-coding regions, with seven regions of high mutation frequency identified. The phylogenetic tree revealed five branches: subgenus Armeniaca, subgenus Microcerasus, subgenus Prunus, subgenus Amygdalus, and subgenus Cerasus. The estimated deviation time for the crown group of Prunus is roughly 61.41 million years ago. Conclusions: This study provides exhaustive genetic evidence for the classification and systematic relationships of the four wild Prunus species and establishes a crucial foundation for subsequent research into the diversity and evolutionary history of the Prunus genus.