Comparative Chloroplast Genomics of Cultivars: Insights into Positive Selection and Population Evolution.

The chloroplast genome, as an important evolutionary marker, can provide a new breakthrough direction for the population evolution of plant species. represents one of the most economically significant and widely cultivated fruit species in the genus In this study, we sequenced and analyzed the complete chloroplast genomes of seven cultivars of to detect the structural variation and population evolutionary characteristics. The total genome size ranged from 156,404 bp ( cv. Hayward) to 156,495 bp ( cv. Yate). A total of 321 simple sequence repeats (SSRs) and 1335 repetitive sequences were identified. Large-scale repeat sequences may facilitate indels and substitutions, molecular variations in varieties' chloroplast genomes. Additionally, four polymorphic chloroplast DNA loci (, , , and ) were detected, which could potentially provide useful molecular genetic markers for further population genetics studies within varieties. Site-specific selection analysis revealed that six genes (, , , , and ) underwent protein sequence evolution. These genes may have played key roles in the adaptation of to various environments. The population evolutionary analysis suggested that cultivars were clustered into an individual evolutionary branch with moderate-to-high support values. These results provided a foundational genomic resource that will be a major contribution to future studies of population genetics, adaptive evolution, and genetic improvement in .