玄参科植物叶绿体基因组特征及系统发育分析  

Chloroplast Genome Characteristics and Phylogenetic Analysis of Scrophulariaceae

作　　者：李斌 苏香萍[1,3] 刘畅 王玉兵 张勇洪 周超 徐青 LI Bin;SU Xiang-ping;LIU Chang;WANG Yu-bing;ZHANG Yong-hong;ZHOU Chao;XU Qing(College of Biological&Pharmaceutical Sciences,China Three Gorges University,Yichang 443002;Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy&College of Basic Medical Science,China Three Gorges University,Yichang 443002;Hangzhou Zhongce Vocational School Qiantang,Hangzhou 310000;School of Basic Medicine,Hubei University of Medicine,Shiyan 442000)

机构地区：[1]三峡大学生物与制药学院,宜昌443002 [2]三峡大学肿瘤微环境与免疫治疗湖北省重点实验室&基础医学院,宜昌443002 [3]杭州市中策职业学校钱塘学校,杭州310000 [4]湖北医药学院基础医学院,十堰442000

出　　处：《生物技术通报》2025年第3期240-254,共15页Biotechnology Bulletin

基　　金：肿瘤微环境与免疫治疗湖北省重点实验室开放基金(2023KZL026);武当特色中药研究湖北省重点实验室开放课题(WDCM2023014)。

摘　　要：【目的】探究玄参科(Scrophulariaceae)叶绿体基因组(chloroplast DNA,cpDNA)的特征及其系统发育关系。【方法】对湖北玄参进行DNA测序,通过组装与注释获得了其叶绿体基因组序列,并从GenBank下载46条玄参科植物叶绿体基因组序列进行比较分析。【结果】玄参科叶绿体基因组长度在142336-154710 bp,GC含量为37.7%-38.1%,展现出典型的四分体结构,其中大单拷贝区长度为83531-97103 bp,小单拷贝区为17375-18600 bp,反向重复区为13497-25695 bp。通过对玄参科叶绿体基因组成的比较,揭示了在进化过程中获得与丢失的模式。此外,共线性分析发现,玄参科叶绿体基因组排列较为保守,但也存在基因组重排事件。长重复序列分析结果显示,玄参科叶绿体基因组大多数是正向重复和回文重复;而简单重复序列分析则鉴定了117-156个SSR位点,其中以A/T组成的单核苷酸重复次数最多,占比高达85.50%-91.50%。通过相对同义密码子使用度(RSCU)分析,筛选出25个最优密码子,绝大部分以A/U结尾。分化时间分析表明,玄参科的共同祖先与近缘物种大约在70.5百万年前(MYA)分开,并在约52.4 MYA形成了一个单系分支,绝大多数玄参科物种出现在近50 MYA。【结论】玄参科叶绿体基因组虽具有相似的结构特征,但在其进化历程中,基因的获得与丢失以及基因组的重排现象亦有所发生。基于叶绿体基因组,构建了更为精细的玄参科系统发育树。此外,分化时间的研究表明,玄参科物种的快速分化主要发生在大约50百万年前。【Objective】To explore the characteristics and phylogenetic relationships of chloroplast genome of the Scrophulariaceae.【Method】The chloroplast genomes of Hubei Scrophularia ningpoensis were sequenced,assembled,and annotated.Additionally,a total of 46 complete chloroplast genomes of Scrophulariaceae were downloaded from GenBank database for comparative analysis.【Result】The full length of the chloroplast genome in Scrophulariaceae ranges from 142336 to 154710 bp,with a GC content between 37.7%and 38.1%.The genome shows a typical quadripartite structure,comprising a large single copy region of 83531 to 97103 bp and a small single copy region of 17375 to 18600 bp,as well as an inverted repeat region spanning 13497 to 25695 bp.Comparative analysis of chloroplast gene composition within the Scrophulariaceae reveals evolutionary patterns of gene gain and loss.Collinearity analysis indicates that the genomic arrangement of the Scrophulariaceae chloroplast genome is relatively conserved,although instances of genome rearrangement events have also been observed.Analysis of long repeat sequences shows that the majority of the Scrophulariaceae chloroplast genome consists of forward repeats and palindromic repeats.Furthermore,simple repeat sequence analysis identified 117 to 156 SSR sites within the Scrophulariaceae chloroplast genome,with single nucleotides composed of A/T being the most frequent,accounting for 85.50%to 91.50%of the total.Relative synonymous codon usage(RSCU)analysis identified 25 optimal codons,the majority of which ended with A/U.Divergence time analysis suggests that the common ancestor of Scrophulariaceae and closely related species diverged approximately 70.5 million years ago(MYA)and formed a monophyletic branch around 52.4 MYA,with most species of Scrophulariaceae appearing nearly 50 MYA.【Conclusion】Although the chloroplast genomes of the Scrophulariaceae demonstrate similar structural characteristics,they have also experienced gene acquisition and loss as well as genome rearrangement e

关 键 词：玄参科 叶绿体基因组 序列特征 系统发育分析 

分 类 号：R28[医药卫生—中药学]