Scholarlink

Background <p><i>Polygonatum kingianum</i>, a key species in traditional Chinese medicine, is increasingly valued for its medicinal and nutritional properties. However, wild resources are declining due to over-exploitation, necessitating genomic studies for conservation.</p> Results <p>Flow cytometry analysis based on genome size revealed the presence of both putative diploid and tetraploid <i>P. kingianum</i>. By further integrating sequencing data from both Illumina and Oxford Nanopore Technologies (ONT), the organelle genomes were assembled. While the chloroplast genomes of different putative ploidy levels of <i>P</i>. <i>kingianum</i> were highly conserved in structure and features, the mitogenome of putative tetraploid <i>P</i>. <i>kingianum</i> consisted of two chromosomes, whereas that of putative diploid <i>P</i>. <i>kingianum</i> contained only one. Mitochondrial gene annotation showed that putative tetraploid <i>P</i>. <i>kingianum</i> possesses one additional copy each of the <i>nad</i>3 and <i>nad</i>5 genes compared to the putative diploid <i>P</i>. <i>kingianum</i>. Analyses of repetitive sequences indicated that, although no obvious correlation was observed between tandem repeats or dispersed repeats and different putative ploidy levels in the chloroplast genomes or between tandem repeats and different putative ploidy levels in the mitogenomes, simple sequence repeats in the organelle genomes correlated with ploidy variation of <i>P</i>. <i>kingianum</i>. Investigation of RNA editing sites revealed ploidy-dependent variations in the <i>cox</i>2 and <i>nad</i>3 genes of the mitogenomes across different ploidy levels of <i>P. kingianum</i>, suggesting that differences in editing sites may be linked to the adaptability of the different ploidies. Phylogenetic analyses based on mitochondrial genes and nucleotide substitution rate analysis showed no significant differences or distinct variations among different ploidy levels of <i>P. kingianum</i>, supporting that the morphologically highly variable <i>P. kingianum</i> comprises only a single species.</p> Conclusions <p>In this study, we successfully assembled the organelle genomes of <i>P. kingianum</i> with different putative ploidy levels and conducted comparative genomic analyses. We found that the mitogenomes of <i>P. kingianum</i> are structurally complex and variable, playing crucial roles in evolution and adaptation. This study not only enhances our understanding of the organelle genome characteristics of different putative ploidy levels within the same species, but also lays the foundation for the subsequent development and utilization of the medicinal value of <i>Polygonatum</i>.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Comprehensive analyses of different putative ploidy levels in organelle genomes of an important medicinal plant Polygonatum kingianum Collett & Hemsl.

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月29日

查看全文
  • Jing Zhao,
  • Zi-Han Chen,
  • Ming-Xian Zhang,
  • Li-Hua Wang,
  • Xiao-Yi Yang,
  • Jia-Guan Wang,
  • You-Yong Zhu,
  • Xing-Yao Li,
  • Yu Zhao

摘要

Background

Polygonatum kingianum, a key species in traditional Chinese medicine, is increasingly valued for its medicinal and nutritional properties. However, wild resources are declining due to over-exploitation, necessitating genomic studies for conservation.

Results

Flow cytometry analysis based on genome size revealed the presence of both putative diploid and tetraploid P. kingianum. By further integrating sequencing data from both Illumina and Oxford Nanopore Technologies (ONT), the organelle genomes were assembled. While the chloroplast genomes of different putative ploidy levels of P. kingianum were highly conserved in structure and features, the mitogenome of putative tetraploid P. kingianum consisted of two chromosomes, whereas that of putative diploid P. kingianum contained only one. Mitochondrial gene annotation showed that putative tetraploid P. kingianum possesses one additional copy each of the nad3 and nad5 genes compared to the putative diploid P. kingianum. Analyses of repetitive sequences indicated that, although no obvious correlation was observed between tandem repeats or dispersed repeats and different putative ploidy levels in the chloroplast genomes or between tandem repeats and different putative ploidy levels in the mitogenomes, simple sequence repeats in the organelle genomes correlated with ploidy variation of P. kingianum. Investigation of RNA editing sites revealed ploidy-dependent variations in the cox2 and nad3 genes of the mitogenomes across different ploidy levels of P. kingianum, suggesting that differences in editing sites may be linked to the adaptability of the different ploidies. Phylogenetic analyses based on mitochondrial genes and nucleotide substitution rate analysis showed no significant differences or distinct variations among different ploidy levels of P. kingianum, supporting that the morphologically highly variable P. kingianum comprises only a single species.

Conclusions

In this study, we successfully assembled the organelle genomes of P. kingianum with different putative ploidy levels and conducted comparative genomic analyses. We found that the mitogenomes of P. kingianum are structurally complex and variable, playing crucial roles in evolution and adaptation. This study not only enhances our understanding of the organelle genome characteristics of different putative ploidy levels within the same species, but also lays the foundation for the subsequent development and utilization of the medicinal value of Polygonatum.