Complete Chloroplast Genomes of Four Oaks from the Section Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus .

is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four section species (. , . , . , and . ) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus . These four chloroplast genomes ranged from 160,784 bp (. ) to 161,632 bp (. ) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other species. We identified seven regions with relatively high variability (, , , , , , and ) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within . Our phylogenetic tree supported the idea that the genus forms two well-differentiated lineages (corresponding to the subgenera and ). Of the three sections in the subgenus , the section was split into two clusters, each nested in the other two sections. Moreover, . and . detected in this study diverged first in the section and mixed with . in the section . In particular, 11 protein coding genes (, , , , , , , , , , and ) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of , which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.