Du Yan, Luo Yang, Wang Yuanyuan, Li Jiaxin, Xiang Chunlei, Yang Meiqing
Baotou Medical College, Baotou 014040, China.
Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
Curr Issues Mol Biol. 2025 Jun 27;47(7):493. doi: 10.3390/cimb47070493.
, a medicinally and economically important genus, is widely used in traditional medicine, agriculture, and horticulture. This study compares the chloroplast genomes of eight East Asian species to assess genetic diversity, structural features, and evolutionary relationships. Complete chloroplast genomes were sequenced, annotated, and analyzed for gene content, codon usage, and repetitive sequences. Phylogenetic relationships were reconstructed using Maximum Likelihood, Maximum Parsimony and Bayesian inference. The genomes exhibited a conserved quadripartite structure (151,081-152,678 bp, GC content 37.9-38.1%), containing 114 unique genes with consistent arrangement. Codon usage favored A/T endings, with leucine (Leu) most frequent and cysteine (Cys) least. We identified 281 long sequence repeats (LSRs) and 345 simple sequence repeats (SSRs), mostly in non-coding regions. Comparative analysis revealed five hypervariable regions (-, -, -, -, ) as potential molecular markers. Phylogenetic analysis confirmed the monophyly of East Asian , dividing them into five clades, with Sect. basal. While G1, G3, and G8 were monophyletic, G5 and G6 were paraphyletic, and the G7-G8 relationship challenged traditional classifications. The genomic evidence provides crucial insights for resolving long-standing taxonomic uncertainties and refining the classification system of . These findings suggest a complex evolutionary history involving hybridization and incomplete lineage sorting, providing valuable genomic insights for phylogeny, taxonomy, and conservation.
是一个具有重要药用和经济价值的属，广泛应用于传统医学、农业和园艺领域。本研究比较了8种东亚物种的叶绿体基因组，以评估遗传多样性、结构特征和进化关系。对完整的叶绿体基因组进行了测序、注释，并分析了基因内容、密码子使用情况和重复序列。使用最大似然法、最大简约法和贝叶斯推断重建了系统发育关系。这些基因组呈现出保守的四分体结构（151,081 - 152,678 bp，GC含量37.9 - 38.1%），包含114个独特基因，排列一致。密码子使用倾向于以A/T结尾，亮氨酸（Leu）出现频率最高，半胱氨酸（Cys）出现频率最低。我们鉴定出281个长序列重复（LSR）和345个简单序列重复（SSR），大多位于非编码区。比较分析揭示了5个高变区（-，-，-，-，-）作为潜在的分子标记。系统发育分析证实了东亚的单系性，将它们分为五个分支，其中 组为基部。虽然G1、G3和G8是单系的，但G5和G6是并系的，G7 - G8的关系挑战了传统分类。基因组证据为解决长期存在的分类学不确定性和完善的分类系统提供了关键见解。这些发现表明其进化历史复杂，涉及杂交和不完全谱系分选，为的系统发育、分类学和保护提供了有价值的基因组见解。
