Structural Variation and Evolutionary Dynamics of Orobanchaceae from the Perspective of the Mitochondrial Genomes Pedicularis kansuensis and Pedicularis chinensis

To better understand the mitochondrial genome evolution within the genus Pedicularis, we investigated two representative species, Pedicularis kansuensis and Pedicularis chinensis. We sequenced and assembled the mitochondrial genomes of two Pedicularis species, P. kansuensis and P. chinensis, using Nanopore technology. Both genomes showed irregular morphological characteristics, with P. chinensis measuring 225,612 bp and P. kansuensis 273,598 bp, and GC (guanine and cytosine) contents of 44.42% and 44.29%, respectively. Each genome encodes 36 unique protein-coding genes, 3 rRNA genes, and varying numbers of tRNA genes (P. chinensis: 20; P. kansuensis: 19). Codon usage analysis revealed distinct preferences, while repeat sequence analysis identified significant differences in SSRs, tandem repeats, and dispersed repeats between the two genomes. Structural analyses highlighted genome recombination facilitated by repeat sequences. Phylogenetic analysis confirmed the placement of Pedicularis within Orobanchaceae, clustering P. kansuensis and P. chinensis with Castilleja paramensis and other genera in the family, thus resolving longstanding taxonomic uncertainties regarding their relationship with Scrophulariaceae. RNA editing events were predominantly C-to-U, ccmB and nad4 exhibiting the highest editing frequencies. Synteny analysis revealed frequent rearrangements, underscoring the dynamic evolution of Pedicularis mitochondrial genomes. These findings provide valuable insights into the structure, function, and evolution of mitochondrial genomes in parasitic plants.