Sequence dynamics and plastome evolution: decoding the complete chloroplast genome of Oenothera drummondii and comparative analysis within Oenothera (Onagraceae)

Abstract

Oenothera species are increasingly valued for their medicinal and ornamental qualities and serve as important models in classical cytoplasmic genetics research. The genus Oenothera L., one of the largest in the Onagraceae family, includes 18 subsections and two deep phylogenetic lineages, Clade A and Clade B. Analyzing high-quality chloroplast genomes can provide crucial insights into species classification and genus-level evolution. In this study, we report the complete chloroplast genome of Oenothera drummondii Hook., the first species from subsection Raimannia, with a total length of 167,177 bp and a GC content of 39.3%. This genome contains 129 genes and displays a typical quadripartite structure. Combining this genome with data from 16 publicly available chloroplast genomes, we conducted a comprehensive comparative and evolutionary analysis. Our results indicate that Clade B species diverged independently from Clade A species. Within Clade A, species from subsection Muniza form a distinct branch, while O. drummondii clusters closely with species from subsection Oenothera. Phylogenetic analysis correlates well with chloroplast genome structural differences, such as the loss of the infA gene in Clade B species, the expansion of the IR regions in Muniza, and a shared large inversion in the LSC region among Raimannia and Oenothera species. We also identified repeat sequences, six highly variable genes, and positively selected genes among the 17 chloroplast genomes analyzed. These findings offer valuable insights into the evolutionary processes of Oenothera species and provide a foundation for the development of future molecular markers based on the identified genes and structural variations.