First complete plastomes of the emblematic Andean tree genus Polylepis Ruiz & Pav. (Rosaceae)

Plastome genomics and phylogenomics are essential tools for understanding plant diversity and evolution. Here we report the complete plastomes of Polylepis australis and P. microphylla, two species of the Andean tree genus Polylepis which forms the world’s highest treelines, using a whole-genome sequencing approach. The assembled plastomes (ca. 155 kb) exhibit the typical quadripartite structure of angiosperms with highly conserved gene content and organization. A total of 117 unique genes (81 protein-coding, 32 tRNA, and 4 rRNA) were annotated in the assembled plastomes. Comparative analysis revealed significant differences from previously reported partial plastomes of Polylepis, which lacked one copy of the inverted repeat (IR) region due to the limitations of long-range PCR methods. Phylogenetic analysis of whole-plastome data of Rosaceae species across subfamilies using Maximum Likelihood (ML) confirmed the monophyly of Polylepis and its placement within the tribe Agrimonieae. Our results highlight the reliability of whole-genome sequencing for generating complete, high-quality plastome sequence information. This provides a foundation for broader phylogenomic studies across the genus to test species boundaries, evaluate hybridization events and evolutionary trajectories, and develop conservation and restoration strategies.