Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features.

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.