Abstract
BACKGROUND: Prunus avium (L.) L. commonly known as sweet cherry, represents an economically significant tree species valued for its fruit production, rootstock potential, and timber quality. With an extensive domestication history spanning centuries, this species has given rise to numerous modern cultivars. Understanding the genomic variation and genetic diversity within P. avium cultivars is crucial for advancing breeding programs and optimizing resource utilization. While the nuclear genome of P. avium has been well characterized, the intraspecific variation of its plastome (plastid genome) remains largely unexplored. In this study, we conducted analyses of 110 plastomes representing 34 genetically distinct sweet cherry cultivars, including 98 newly assembled plastomes from varieties cultivated in China. RESULTS: The complete plastomes ranged in size from 157,667 to 157,987 base pairs, with a consistent GC content of approximately 36.7%. Phylogenetic reconstruction, and principal component analysis (PCA) consistently identified three major lineages, two of which displayed remarkably low genetic diversity. Among the 110 P. avium accessions, we identified 11 distinct plastid haplotypes, with approximately 70% accessions sharing a common haplotype (Hap2). Comparative analysis demonstrated significantly reduced genetic diversity in modern cultivars compared to landraces and wild accessions, reflecting extensive clonal propagation in commercial breeding programs. Furthermore, we identified lineage-specific mutation hotspots and developed potential molecular markers for cultivar discrimination. CONCLUSIONS: This study elucidates the evolutionary patterns and plastomic architectureof China's predominant cultivated sweet cherry varieties. These findings provide a critical bridge toward comprehensive cherry pan-plastome research while establishing foundational insights into the domestication history of this economically significant species.