Mitochondrial genome assembly, comparative analysis of two caprifoliaceae species, and insights into adaptive evolution

Caprifoliaceae is a cosmopolitan plant family encompassing a large number of species, with significant economic and ecological values. Species divergence and adaptation in Caprifoliaceae are not well understood due to extensive hybridization and rapid radiation. Here, we assembled and compared the complete mitochondrial genomes of Kolkwitzia amabilis and Triplostegia glandulifera, which are distributed in distinct habitats with unique life forms, to elucidate the structural variation of mitogenomes and their implications for species divergence and environmental adaptation. The mitochondrial genome of K. amabilis consists of two circular molecules with sizes of 540,375 bp and 197,940 bp, respectively, while T. glandulifera has a single circular genome of 642,933 bp. The two genomes exhibit a similar preference for A/U bases in codon usage, mainly driven by natural selection, but present significant differences in mode and the number of repeat types. Among 25 shared genes in six Caprifoliaceae species, atp1 had the highest nucleotide diversity; meanwhile, atp4, ccmB, and mttB were under positive selection. Notably, rps7 in T. glandulifera had potentially undergone species-specific positive selection. A phylogenetic tree of Caprifoliaceae species based on 19 conserved protein-coding genes (PCGs) showed that K. amabilis and T. glandulifera formed a sister group, providing molecular evidence at the mitogenome level for the systematic classification of plants in this family. Furthermore, analyses of ancestral genome reconstruction indicated that both mitogenomes exhibited significant gene order rearrangements and gene deletions, and their duplication patterns of nad1 and nad2 genes differed from those of other Caprifoliaceae species, suggesting that dynamic structural changes were an important feature of mitogenome evolution in Caprifoliaceae. In conclusion, the firstly reported mitogenomes of two distinctive species provided important molecular data for phylogenetic, genomic evolution, potential divergence and adaption in Caprifoliaceae.