目的 解析百合科贝母属Fritillaria多年生药用植物太白贝母Fritillaria taipaiensis叶绿体全基因组的结构特征，探究其系统发育关系。方法 采用CTAB法提取太白贝母叶片基因组DNA，基于Illumina novaseq X plus平台进行测序，使用GetOrganelle组装叶绿体基因组，利用生物信息学方法比较中药材川贝母6种基原药用植物叶绿体基因组之间的结构特征及变异程度，并通过MEGA11.0软件以邻接（neighbor-joining，NJ）法构建系统发育树。结果 太白贝母叶绿体基因组全长151 700 bp，包括1个大单拷贝区（large single copy，LSC），1个小单拷贝区（small single copy，SSC）和1对反向重复区（inverted repeats，IRa和IRb），GC含量为36.97%。太白贝母叶绿体基因组共注释到131个基因，其中包含8个rRNA、38个tRNA、84个蛋白编码基因和1个假基因。密码子使用偏好分析显示，50.00%的密码子相对使用度大于1，且偏好以A/T结尾。共鉴定216个简单重复序列（simple sequence repeats，SSR），其中单核苷酸重复占比最高（52.78%），且主要由A和T构成，表明A/T碱基使用频率较高。边界比较分析表明，6种川贝母基原植物（川贝母、瓦布贝母、梭砂贝母、太白贝母、暗紫贝母和甘肃贝母）的叶绿体基因组边界结构保守。变异分析和共线性分析则揭示，6种川贝母基原植物叶绿体基因组变异程度较低，且均存在一个保守共线区块。系统发育分析中，贝母属9个物种聚为一支，其中6种川贝母基原物种再形成独立分支，贝母属与百合属互为姐妹支，与老鸦瓣属区分开来。结论 成功组装了高质量的太白贝母叶绿体基因组，为其遗传结构解析与多样性研究提供了基础。

Objective To analyze the structural characteristics of the complete chloroplast genome of the perennial medicinal plant Fritillaria taipaiensis, a species of the genus Fritillaria in the Liliaceae family, and investigate its phylogenetic relationships. Methods Genomic DNA was extracted from leaves of F. taipaiensis using the CTAB method. Sequencing was performed on the Illumina HiSeq platform, followed by chloroplast genome assembly with GetOrganelle. Using bioinformatics methods to compare the structural characteristics and degree of variation among the chloroplast genomes of six original medicinal plants of F. Cirrhosa. A phylogenetic tree was constructed by the neighbor-joining method (NJ) using MEGA11.0. Results The complete chloroplast genome of F. taipaiensis is 151 700 bp in length, comprising a large single-copy (LSC, 81 456 bp) region, a small single-copy (SSC, 17 554 bp) region, and a pair of inverted repeats (IRa and IRb, 26 345 bp), with a GC content of 36.97%. A total of 131 genes were annotated, including 8 rRNA genes, 38 tRNA genes, 84 protein-coding genes, and one pseudogene. Codon usage bias analysis indicated that 50.00% of codons had a relative synonymous codon usage (RSCU) value greater than 1, with a preference for A/T endings. In total, 216 simple sequence repeats (SSRs) were identified, among which mononucleotide repeats were the most abundant (52.78%), predominantly composed of A and T, suggesting a high frequency of A/T base usage. Comparative boundary analysis revealed conserved chloroplast genome structures across six original species of F. Cirrhosa (F. cirrhosa, F. wabuensis, F. delavayi, F. taipaiensis, F. unibracteata, and F. przewalskii). Variation and collinearity analyses indicated low degree of variation of chloroplast genome and the presence of a conserved collinear block among these six species. Phylogenetic analysis showed that all nine Fritillaria species clustered into one clade, with the six original species of F. Cirrhosa forming a distinct subclade, the genus Fritillaria and Lilium are sister branches of each other, but should be distinguished from the genus Amana Honda. Conclusion This study successfully assembled a high-quality chloroplast genome of F. taipaiensis, providing a foundation for research on its genetic structure and diversity.

R286.012

国家重点研发计划（2023YFD1600402）；陕西省中医药管理局项目（2025-CXTD-01，2021-QYZL-02）；陕西省科技厅社发重点项目（2025ZY-XCZXJX-04、2024SF-GJHX-05）；中央本级重大增减支项目（2060302）；陕西中医药大学“秦药”品质评价及资源开发学科创新团队项目（2019-QN01）