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<p>Ginseng (<i>Panax ginseng</i>) is a medicinal plant of considerable medical and economic interest. However, preserving its genetic stability and targeted selection pose challenges that limit the effective conservation and use of its genetic resources. This study aims to systematically elucidate the structural characteristics, evolutionary patterns, and phylogenetic relationships of the ginseng mitochondrial genome, in order to create a theoretical basis for the conservation of ginseng genetic resources and the acceleration of molecular selection processes. Using PacBio HiFi and DNBSEQ-T7 short-read sequencing, we assembled the complete mitochondrial genome of the BT cultivar (~ 465&#xa0;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 (<i>nad4</i>, <i>cox2</i>) exhibited positive selection signals. Phylogenetic analysis confirmed close relationships between ginseng and <i>P. quinquefolius</i>, with <i>P. notoginseng</i> forming a distinct clade. A mitochondrial genome variation map was constructed by integrating data from six ginseng populations. Analysis of this comparative mitochondrial genome revealed high genetic stability across populations, with SNPs, InDels, and structural variations identified. These findings not only clarify the structural features, evolutionary dynamics, and population variation patterns of the <i>P. ginseng</i> mitochondrial genome but also provide key genetic resources and molecular markers for high-resolution phylogenetic analysis of Araliaceae, functional research on mitochondrial genomes of medicinal plants, and targeted breeding of <i>P. ginseng</i> varieties, which is of great significance for promoting the conservation and sustainable utilization of ginseng germplasm resources.</p>

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Comparative mitochondrial genome analysis of Panax ginseng reveals structural variation and genetic diversity

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月29日

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  • Yidan Xi,
  • Xuejiao Liao,
  • Haoyu Hu,
  • Shuai Guo,
  • Wei Shang,
  • Shuang Liu,
  • Tae-Jin Yang,
  • Shilin Chen,
  • Jiang Xu,
  • Deqiang Dou

摘要

Ginseng (Panax ginseng) is a medicinal plant of considerable medical and economic interest. However, preserving its genetic stability and targeted selection pose challenges that limit the effective conservation and use of its genetic resources. This study aims to systematically elucidate the structural characteristics, evolutionary patterns, and phylogenetic relationships of the ginseng mitochondrial genome, in order to create a theoretical basis for the conservation of ginseng genetic resources and the acceleration of molecular selection processes. Using PacBio HiFi and DNBSEQ-T7 short-read 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 mitochondrial genome variation map was constructed by integrating data from six ginseng populations. Analysis of this comparative mitochondrial genome revealed high genetic stability across populations, with SNPs, InDels, and structural variations identified. These findings not only clarify the structural features, evolutionary dynamics, and population variation patterns of the P. ginseng mitochondrial genome but also provide key genetic resources and molecular markers for high-resolution phylogenetic analysis of Araliaceae, functional research on mitochondrial genomes of medicinal plants, and targeted breeding of P. ginseng varieties, which is of great significance for promoting the conservation and sustainable utilization of ginseng germplasm resources.