The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China.
Sci Rep. 2023 Oct 1;13(1):16495. doi: 10.1038/s41598-023-43638-1.
The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.
黄精属是百合科的多年生草本植物，具有重要的经济和药用价值。大多数黄精植物表现出显著的相似性，缺乏独特的鉴别特征，因此导致市场上掺杂药用材料的情况增多。在这项研究中，我们对四种黄精植物的完整叶绿体（cp）基因组进行了深入分析，并与四种密切相关的物种进行了比较。主要目的是揭示结构变异、物种分化以及分类群之间的系统发育关系。四种黄精植物的 cp 基因组具有典型的四部分结构，包括一个大的单一拷贝区域（LSC）、一个小的单一拷贝区域（SSC）和一对反向重复区域。总共我们注释了 131 到 133 个基因，包括 84 到 86 个蛋白质编码基因、38 个转移 RNA（tRNA）基因、8 个核糖体 RNA（rRNA）基因和 0 到 2 个假基因（ycf1、infA）。我们的比较分析明确揭示了黄精属内基因排列和 GC 含量的显著一致性。此外，我们预测了 22 个蛋白质编码基因中存在 59 到 64 个潜在的 RNA 编辑位点，其中 ndhB 基因的 RNA 编辑位点最为突出，有 15 个位点。值得注意的是，确定了六个具有较大潜在可变性的区域，其特征是 Pi 值升高。值得注意的是，鉴定黄精属内物种的分子标记、种群遗传研究和系统发育分析分别在 psaJ-rpl33 和 trnS+trnT-psaD 条形码中得到了确定。由此产生的系统发育树明确描绘了在百合科的进化框架内形成的一个单系进化枝，表明与 Maianthemum、Dracaeneae 和 Asparageae 具有更密切的进化亲缘关系。本研究全面概述了发现结果，为分子物种鉴定、系统发育关系阐明以及为黄精属物种量身定制的 DNA 条形码的建立提供了依据。
