A comprehensive analysis of 14 chloroplast genomes from the subfamily Apocynoideae (Apocynaceae)

The subfamily Apocynoideae comprises diverse woody vines and shrubs that play important ecological, medicinal, and ornamental roles, with Nerium oleander being one of the representative species. Analyzing the chloroplast genomes of this subfamily provides a molecular foundation for phylogenetic reconstruction, species identification, and breeding programs. In this study, we conducted a comprehensive comparative analysis of 14 chloroplast genomes in Apocynoideae, including the two newly sequenced genomes of N. oleander cultivars 'Paihua' and 'Nanum'. Our results revealed that: (1) the chloroplast genome structure within this subfamily exhibits significant variations in the non-coding regions; (2) codon usage is influenced by both mutational pressure and natural selection, with lineage-specific fine-tuning; and (3) selection pressure follows an evolutionary pattern characterized by core conservation and specific divergence, while repetitive sequences display distinct species-specific features and a notable A/T-rich bias. Phylogenetic analysis showed that N. oleander shares a close relationship with Strophanthus. Furthermore, the subfamily Apocynoideae is non-monophyletic, with the subfamily Asclepiadoideae nested within it as a clade. This study provides the first comprehensive multi-dimensional evolutionary analysis of chloroplast genomes in Apocynoideae, offering important molecular evidence for lineage differentiation, adaptive evolution, and species identification.