Journal Article

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

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

2026

Overview

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 nad 3 and nad 5 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 cox 2 and nad 3 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 .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Annotations / Biomedical and Life Sciences / Botanical research / Chloroplasts / Chromosomes / Cyclooxygenase-2 / Diploids / Editing / Flow cytometry / Genes / Genetic aspects / Genetic testing / Genome, Chloroplast - genetics / Genome, Mitochondrial - genetics / Genome, Plant / Genomes / Genomic analysis / Herbal medicine / Life Sciences / Medicinal plants / Nucleotide sequence / Nucleotides / Organelles / Phylogenetics / Phylogeny / Physiological aspects / Plant genetics / Plant organelles / Plant Sciences / Plants, Medicinal - genetics / Ploidies / Ploidy / Polygonatum / Polygonatum - genetics / Proteins / RNA editing / Simple sequence repeats / Traditional Chinese medicine / Tree Biology / Variation