Phylogenetic aspects, hotspots of nucleotide divergence, highly divergent genes, and specific RNA editing sites have been identified and characterized in the plastomes of the subgenus Passiflora.

The genus Passiflora comprises more than 500 species across five subgenera: Astrophea, Decaloba, Deidamioides, Passiflora, and Tetrapathea. The most economically relevant species belong to the subgenus Passiflora, whose genetic pool and diversity among wild species remain poorly characterized. Similarly, little is known about the interspecific relationships within the subgenus Passiflora and the genetic causes of nuclear-cytoplasmic incompatibility observed in interspecific hybrids. Here, we report the complete nucleotide sequences of six plastomes belonging to species of the subgenus Passiflora, with the aim of better understanding the evolution of the plastome in this subgenus. Complete plastome sequences revealed five hotspots of nucleotide polymorphism: three intergenic regions and two coding sequences. Moreover, among 70 RNA editing sites predicted in our analysis for the subgenus Passiflora, 38 were not shared by all analyzed species, highlighting their species-specific occurrence. Furthermore, phylogenies based on plastid sequences accurately resolved most relationships between species and suggested a non-monophyletic origin of three super-sections of the subgenus Passiflora, previously defined solely based on morphological traits. Finally, our findings identified putative candidates, including predicted RNA editing sites and the coding sequences of accD and clpP genes, responsible for nuclear-cytoplasmic incompatibility in the interspecific hybrids of Passiflora.

系统发育方面，核苷酸分歧的热点，高度分歧的基因和特定的RNA编辑位点已被鉴定和表征在西番莲属的质体中。

属西番莲包含多于500种在五个亚属：Astrophea，Decaloba，Deidamioides，西番莲，和Tetrapathea。经济上最相关的物种属于西番莲亚属，其遗传库和野生物种之间的多样性仍然缺乏特征。同样，关于西番莲属内种间关系和种间杂种中观察到的核-细胞质不相容性的遗传原因知之甚少。在这里，我们报告属于西番莲属物种的六个质体组的完整核苷酸序列，目的是更好地了解该亚属中质体组的进化。完整的质体序列揭示了核苷酸多态性的五个热点：三个基因间区域和两个编码序列。此外，在我们对西番莲亚属的分析中预测的70个RNA编辑位点中，并非38个不是所有被分析的物种共有的，突出了它们特定物种的出现。此外，基于质体序列的系统发育正确地解决了物种之间的大多数关系，并提出了西番莲亚属的三个超节的非单系起源，以前仅根据形态学特征对其进行了定义。最后，我们的发现确定了可能的候选基因，包括预测的RNA编辑位点和accD的编码序列和clpP基因，负责西番莲种间杂种的核质不相容性。