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Background <p>The genus <i>Polygonatum</i> had high scientific research and economic value due to its edible and medicinal properties. In China, Yuzhu (<i>Polygonatum odoratum</i>) and Huangjing (including <i>P. cyrtonema</i>, <i>P. sibiricum</i> and <i>P. kingianum</i>) were the traditional medicines with very long history of utilization and cultivation. However, the lack of a reported mitochondrial genome (mitogenome) for <i>P. odoratum</i> has severely restricted our understanding of the organelle evolution within the genus <i>Polygonatum</i>.</p> Results <p>In the present studywe integrated Oxford Nanopore long-read and Illumina short-read sequencing to generate a complete mitogenome assembly of <i>P. odoratum</i>. The assembled mitogenome was represented by a circular ring molecule with the full-length of 720,613&#xa0;bp. The mitogenome encoded 35 protein-coding genes (PCGs), 3 ribosome RNAs (rRNAs) and 20 transfer RNAs (tRNAs). Repeat element analysis generated a total of 220 simple sequence repeats (SSRs), 22 tandem repeats and 388 pairs of dispersed repeats. In addition, 584 RNA editing sites were identified, and 22 sites were verified by PCR amplifications and Sanger sequencing. 31 mitochondrial plastid DNAs (MTPTs) between the chloroplast genome (cpgenome) and mitogenome of <i>P. odoratum</i> were identified, accounting for 1.32% of <i>P. odoratum</i> mitogenome length. Phylogenetic analysis according to the mitogenomes and cpgenomes reflected a similar taxonomic and evolutionary status of <i>P. odoratum</i>. Additionally, compared with the PCGs of “fossilized” <i>Liriodendron tulipifera</i>, the mitogenome of <i>P. odoratum</i> lost 5 genes (<i>rpl2</i>, <i>rpl10</i>, <i>rps7</i>, <i>rps11</i> and <i>sdh3</i>). The following selective pressure analysis indicated that, the mitogenomes of <i>P. odoratum</i> and the selected species had a conservative evolutionary pattern, and the 12 core genes were subjected to strictly selective constraints.</p>

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Assembly and comparative analysis of the complete mitochondrial genome of Polygonatum odoratum (Yuzhu), a medicine-food homologous plant

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月1日

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  • Luyun Ning,
  • Tianhao Fu,
  • Jiahui Yi,
  • Jianmei Gan,
  • Guozhen Xie,
  • Yeman Liu,
  • Limin Gong,
  • Wei Wang

摘要

Background

The genus Polygonatum had high scientific research and economic value due to its edible and medicinal properties. In China, Yuzhu (Polygonatum odoratum) and Huangjing (including P. cyrtonema, P. sibiricum and P. kingianum) were the traditional medicines with very long history of utilization and cultivation. However, the lack of a reported mitochondrial genome (mitogenome) for P. odoratum has severely restricted our understanding of the organelle evolution within the genus Polygonatum.

Results

In the present studywe integrated Oxford Nanopore long-read and Illumina short-read sequencing to generate a complete mitogenome assembly of P. odoratum. The assembled mitogenome was represented by a circular ring molecule with the full-length of 720,613 bp. The mitogenome encoded 35 protein-coding genes (PCGs), 3 ribosome RNAs (rRNAs) and 20 transfer RNAs (tRNAs). Repeat element analysis generated a total of 220 simple sequence repeats (SSRs), 22 tandem repeats and 388 pairs of dispersed repeats. In addition, 584 RNA editing sites were identified, and 22 sites were verified by PCR amplifications and Sanger sequencing. 31 mitochondrial plastid DNAs (MTPTs) between the chloroplast genome (cpgenome) and mitogenome of P. odoratum were identified, accounting for 1.32% of P. odoratum mitogenome length. Phylogenetic analysis according to the mitogenomes and cpgenomes reflected a similar taxonomic and evolutionary status of P. odoratum. Additionally, compared with the PCGs of “fossilized” Liriodendron tulipifera, the mitogenome of P. odoratum lost 5 genes (rpl2, rpl10, rps7, rps11 and sdh3). The following selective pressure analysis indicated that, the mitogenomes of P. odoratum and the selected species had a conservative evolutionary pattern, and the 12 core genes were subjected to strictly selective constraints.