Luo Haoxiang, Ren Fengxiao, Cao Guochao, Wang Dekai, Jia Qiaojun
College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, PR China.
BMC Plant Biol. 2025 Aug 21;25(1):1109. doi: 10.1186/s12870-025-07074-9.
Polygonatum cyrtonema Hua, a valuable medicinal and edible plant in China, has been increasingly cultivated to produce nutritional and health products to meet market demand. However, the absence of the mitochondrial genome hinders the research of evolutionary analysis, artificial cultivation, and medicinal resource development. This study aimed to systematically characterize the mitochondrial genome of P. cyrtonema and perform a preliminary bioinformatic analysis.
In this study, the mitochondrial genome of P. cyrtonema was assembled and annotated by combining Illumina reads with long-read Oxford Nanopore Technologies, which formed a complex non-circular structure covering 664,991 bp in length, with 33 protein-coding genes, 20 tRNAs, and 3 rRNAs. Overall, a total of 194 simple repeats, 24 tandem repeats, and 294 dispersed repeats were identified, and 599 RNA editing sites were predicted, all of which were C-to-T types. In particular, 29 homologous fragments between the chloroplast and mitochondrial genome were detected and accounted for 2.4% of the mitochondrial genome. In addition, codon usage analysis, nucleotide diversity analysis, and Ka/Ks analysis suggested a slower rate of evolution and a relatively conserved structure of the mitochondrial genome. Phylogenetic relationships based on 33 species demonstrated that P. cyrtonema was most closely related to Polygonatum sibiricum.
Our results provide comprehensive information on the mitochondrial genome of P. cyrtonema, and demonstrate the availability of mitochondrial genome-based taxonomic classification for Polygonatum Mill.. Moreover, it offers a valuable foundation for future research in the cultivation and pharmacological development within Polygonatum species.
黄精是我国一种珍贵的药食两用植物，为满足市场需求，其人工栽培规模日益扩大，用于生产营养保健品。然而，线粒体基因组的缺失阻碍了其进化分析、人工栽培及药用资源开发等方面的研究。本研究旨在系统解析黄精线粒体基因组，并进行初步的生物信息学分析。
本研究结合Illumina测序 reads 和长读长 Oxford Nanopore Technologies 技术对黄精线粒体基因组进行了组装和注释，其形成了一个复杂的非环状结构，长度为664,991 bp，包含33个蛋白质编码基因、20个tRNA和3个rRNA。共鉴定出194个简单重复序列、24个串联重复序列和294个分散重复序列，预测到599个RNA编辑位点，均为C-to-T类型。特别地，检测到叶绿体和线粒体基因组之间有29个同源片段，占线粒体基因组的2.4%。此外，密码子使用分析、核苷酸多样性分析和Ka/Ks分析表明，线粒体基因组进化速率较慢，结构相对保守。基于33个物种构建的系统发育关系表明，黄精与玉竹亲缘关系最近。
我们的研究结果提供了黄精线粒体基因组的全面信息，证明了基于线粒体基因组的黄精属分类的可行性。此外，为黄精属植物未来的栽培和药理开发研究提供了有价值的基础。
