Evolutionary dynamics and phylogenetic analysis of the mitochondrial genome of the medicinal plant Peucedanum praeruptorum

Peucedanum praeruptorum (Apiaceae) is a medicinal plant of significant value, yet the specific features of its mitochondrial architecture and evolutionary history remain largely unexplored. This study was aimed to characterize the complete mitogenome of P. praeruptorum to elucidate its genomic organization and evolutionary dynamics within the Apiaceae family. The complete mitogenome of P. praeruptorum was assembled into a genome size of 214,529 bp with a GC content of 44.9%, encoding 58 genes, including 36 protein-coding genes (PCGs), 19 tRNAs, and 3 rRNAs. Distinct from many related angiosperms, this genome displays a compact size characterized by limited accumulation of repetitive sequences and a high degree of gene integrity, with rpl16 being one of the few losses among conserved genes typically found in this family. Codon usage analysis revealed a bias towards A/T-ending codons, shaped by a complex interplay of mutational pressure and natural selection. A total of 666 predicted RNA editing sites was identified, with a pronounced heterogeneous distribution favoring complex I subunits (nad genes) over ribosomal protein genes. Selection pressure analyses indicated that five mitochondrial PCGs are under strong purifying selection. Using a phylogeny-based branch-site model, significant evidence of positive selection was detected for matR and rpl10 along the P. praeruptorum lineage. Phylogenetic analysis robustly placed P. praeruptorum within the subfamily Apioideae, forming a sister relationship with a clade comprising Angelica, Cnidium, and Dystaenia. This study presents a comprehensive characterization of the P. praeruptorum mitogenome, highlighting an evolutionary strategy that favors structural compactness while preserving essential gene content. These findings elucidate the roles of repetitive elements in genome size variation, the uneven distribution of predicted RNA editing, and the impact of positive selection on specific mitochondrial genes. This work provides a valuable genomic resource for resolving the complex phylogenetic relationships and understanding mitochondrial evolution within the Apiaceae family.