Comparative Chloroplast Genomics of Actinidia deliciosa 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. <i>Actinidia deliciosa</i> represents one of the most economically significant and widely cultivated fruit species in the genus <i>Actinidia.</i> In this study, we sequenced and analyzed the complete chloroplast genomes of seven cultivars of <i>Actinidia. deliciosa</i> to detect the structural variation and population evolutionary characteristics. The total genome size ranged from 156,404 bp (<i>A. deliciosa</i> cv. Hayward) to 156,495 bp (<i>A. deliciosa</i> 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 <i>A. deliciosa</i> varieties' chloroplast genomes. Additionally, four polymorphic chloroplast DNA loci (<i>atpF-atpH</i>, <i>atpH-atpI</i>, <i>atpB</i>, and <i>accD</i>) were detected, which could potentially provide useful molecular genetic markers for further population genetics studies within <i>A. deliciosa</i> varieties. Site-specific selection analysis revealed that six genes (<i>atpA</i>, <i>rps3</i>, <i>rps7</i>, <i>rpl22</i>, <i>rbcL,</i> and <i>ycf2</i>) underwent protein sequence evolution. These genes may have played key roles in the adaptation of <i>A. deliciosa</i> to various environments. The population evolutionary analysis suggested that <i>A. deliciosa</i> 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 <i>Actinidia</i>.