Pan-Mitochondrial Genomic Analysis of Ginseng (Panax ginseng) Reveals Structural Variation, Phylogenetic Relationships, and Genetic Diversity

Ginseng (Panax ginseng), a vital medicinal plant, faces challenges in genetic stability and directed breeding. This study aimed to elucidate mitochondrial genome structure, evolution, and phylogenetic relationships to guide germplasm conservation and molecular breeding. Using PacBio HiFi and Illumina sequencing, we assembled the complete mitochondrial genome of the BT cultivar (~ 465 kb, 55% A + T, encoding 80 functional genes). Repetitive sequences and codon usage patterns (preference for G/C at third codon positions) were characterized. Selective pressure analysis showed that most genes underwent purifying selection, but respiratory chain genes (nad4, cox2) exhibited positive selection signals. Phylogenetic analysis confirmed close relationships between ginseng and P. quinquefolius, with P. notoginseng forming a distinct clade. A pan-mitochondrial genome was constructed by integrating data from six ginseng populations. Analysis of this pan-genome revealed high genetic stability across populations, with SNPs, InDels, and structural variations identified. These findings provide insights into mitochondrial conservation, adaptive evolution, and population variation, supporting targeted breeding strategies for ginseng varieties.