目的 以黄花地黄Rehmannia chrysantha为材料进行高通量测序，明确黄花地黄叶绿体基因组的结构及其与近缘物种的系统发育关系。方法 使用CodonW v1.3软件对黄花地黄叶绿体进行密码子偏好性分析，导入IRscope、mVISTA软件，分析黄花地黄与其同属物种序列变异情况，用MEGA11软件构建地黄属及其近缘属的系统发育树。结果 黄花地黄叶绿体基因组全长153 789 bp，是典型的环状双链四分体结构，其中有28个密码子的使用频率较高，中性绘图分析、ENC-plot分析及PR2-plot分析表明黄花地黄密码子使用偏好性主要受自然选择影响。地黄属IR边界有不同程度的变化，且主要集中于JLA、JLB。rpl2、psbI、petN、psbZ、ycf1、ndhB可分别作为鉴别地黄同属植物的DNA条形码序列。系统发育树表明黄花地黄与地黄亲缘关系较近。结论 地黄属叶绿体基因组蛋白编码基因倾向于使用A/U碱基编码的密码子，自然选择是影响密码子偏好性的主要因素。研究结果可为地黄属的分子进化、系统发育及叶绿体基因工程提供参考。

Objective High-throughput sequencing of Rehmannia chrysantha L.was performed to elucidate the structure of its chloroplast genome and its phylogenetic relationship with related species. Methods Codon preference analysis of chloroplasts of R. chrysantha was performed using CodonW v1.3 software. The codon usage bias was analyzed by using CodonW v1.3 software. Then, the obtained data were imported into IRscope and mVISTA to clarify sequence variations between R. chrysantha and related species. This study constructed a phylogenetic tree of the genus Rehmannia and its related genera on MEGA11 software. Results The chloroplast genome of R. chrysantha was a typical circular double-stranded molecule with a quadripartite structure and a total length of 153 789 bp. It has 28 high-frequency codons. Neutral plot analysis, ENC-plot analysis, and PR2-plot analysis all indicated that natural selection was the main cause of codon usage bias in R. chrysantha. It was also found that there were varying degrees of variation in the inverted repeat (IR) boundaries of the Rehmannia genus, and these changes were mainly concentrated in JLA and JLB. The genes rpl2, psbI, petN, psbZ, ycf1, and ndhB were identified as potential DNA barcodes for distinguishing closely related genus Rehmannia. In addition, phylogenetic analysis revealed a close evolutionary relationship between R. chrysantha and R. glutinosa L. Conclusion Protein-coding genes in the chloroplast genomes of genus Rehmannia exhibited a preferential use of codons ending in A/U, with natural selection being the primary factor influencing this codon usage bias. These findings will provide a foundation for future studies on molecular evolution, phylogeny, and chloroplast genetic engineering within this genus.

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山西省中药材产业技术体系（2026）；山西省科技创新人才团队专项（202304051001020）；山西中医药大学2025年研究生实践创新项目（X2025SJ036）