宽叶十万错叶绿体基因组比较分析和系统进化关系研究  

Comparative analysis and phylogenetic relationship of complete chloroplast genomes in Asystasia gangetica

作　　者：赵艳林 陈渊 沈晓婷 安昌 王振华 黄泽豪[1] 黄鸣清[1] 林彦翔 郑燕芳[1] ZHAO Yanlin;CHEN Yuan;SHEN Xiaoting;AN Chang;WANG Zhenhua;HUANG Zehao;HUANG Mingqing;LIN Yanxiang;ZHENG Yanfang(College of Pharmacy,Fujian University of Traditional Chinese Medicine,Fuzhou 350122,China;Fujian Key Laboratory of Haixia Plant Application Systems Biology,College of Life Sciences,Fujian Agriculture and Forestry University,Fuzhou 350002,China;Engineering Technology Research Center of Characteristic Medicinal Plants of Fujian,School of Biological Science and Engineering,Ningde Normal University,Ningde 352100,China)

机构地区：[1]福建中医药大学药学院,福建福州350122 [2]福建农林大学生命科学学院福建省海峡植物应用系统生物学重点实验室,福建福州350002 [3]宁德师范学院生物科学与工程学院,福建省特色药用植物工程技术研究中心,福建宁德352100

出　　处：《中草药》2025年第5期1731-1746,共16页Chinese Traditional and Herbal Drugs

基　　金：国家自然科学基金项目(32100168);福建省自然科学基金项目(2021J05061);福建中医药大学基础类学科科研提升计划项目(XJC2023008);福建中医药大学校管课题(X2023025);福建中医药大学高层次人才科研启动资金项目(X2020012-人才)。

摘　　要：目的以药用植物宽叶十万错Asystasia gangetica为研究对象,解析其叶绿体基因组结构特征,探究宽叶十万错在爵床族中的系统发育关系;方法利用Illumina NovaSeq 6000测序平台对宽叶十万错叶绿体基因组进行测序,对其进行组装、注释和特征序列分析,并基于34种爵床族物种构建系统发育树。结果宽叶十万错叶绿体基因组为典型的四分体结构,总序列长度为150307 bp,包括一个大单拷贝区(LSC,82332 bp),一个小单拷贝区(SSC,17425 bp)和一对反向重复区(IRs,25275 bp);宽叶十万错叶绿体基因组共注释到光合作用基因、自我复制基因、其他基因和未知功能基因4类共133个基因,包括88个蛋白编码基因,37个tRNA基因和8个rRNA基因;宽叶十万错叶绿体基因组共检测到34个SSR位点,SSR类型以A/T为主,通过REPuter软件共检测到33个长重复序列;IR区边界分析表明,宽叶十万错比其他属物种保守,边界区域变异小;基于8个属8个物种全叶绿体基因组比较分析可知,基因间隔区atpH-atpI、petN-trnD-GUC、rps4-trnT-UGU、trnF-GAA-ndhJ等的变异大于编码区;宽叶十万错密码子偏好性分析表明,甘氨酸是宽叶十万错使用频次最高的氨基酸,以A或U结尾的密码子是宽叶十万错叶绿体基因组的偏好性密码子;ENC、PR2和中性绘图分析表明,自然选择是影响宽叶十万错密码子偏好性的主要原因;选择压力分析表明,有9个基因受到正选择,对宽叶十万错及其近缘属物种适应性进化具有重要作用;系统发育分析表明,宽叶十万错所在的十万错属和钩粉草属形成姊妹类群,亲缘关系最近,并具有较高的支持率,共同归为彩叶木亚族。结论对宽叶十万错叶绿体基因组结构进行了解析,并探讨了爵床族物种系统发育关系,丰富了爵床族药用植物遗传资源,为爵床族的物种分类提供了参考。Objective To analyze the structural features of the chloroplast genome in medicinal plant Asystasia gangetica and explore its phylogenetic relationships in the tribe Justiceae.Methods The chloroplast genome sequence of A.gangetica was obtained by sequencing with Illumina NovaSeq 6000,and assembled,annotated and analyzed the characteristic sequences of the genome.A phylogenetic tree was constructed based on 34 species of the tribe Justiceae.Results The chloroplast genome of A.gangetica exhibits a typical tetrad structure with a length of 150307 bp,including a large single-copy region(LSC,82332 bp),a small single-copy region(SSC,17425 bp),and a pair of inverted repeat regions(IRs,25275 bp).The chloroplast genome of A.gangetica has been annotated with 133 genes in four categories:photosynthesis genes,self-replication genes,other genes and unknown functional genes,comprising 88 protein-coding genes,37 tRNA genes and eight rRNA genes.A total of 34 SSR loci were detected in the chloroplast genome of A.gangetica,with A/T being the predominant SSR type;REPuter software identified 33 long repeat sequences;Analysis of IR boundaries indicated that A.gangetica was more conservative than other species,with minimal variation in the boundary region.Based on the comparative analysis of complete chloroplast genomes of eight species from eight genera,it can be concluded that the variation rates of atpH-atpI,petN-trnD-GUC,rps4-trnT-UGU,trnF-GAA-ndhJ etc in gene spacer regions were the highest.The codon usage bias analysis of A.gangetica indicated that glycine was the most frequently used amino acid in A.gangetica,and codons ending in A or U had a strong impact on codon perference.The ENC,PR2,and neutrality plot analyses indicated that natural selection was the primary factor influencing codon preference in A.gangetica.The selective pressure analysis revealed that nine genes were under positive selection,playing a crucial role in the adaptive evolution of A.gangetica and its closely related species.Phylogenetic analysis indicated th

关 键 词：宽叶十万错 叶绿体基因组 密码子偏好性 选择压力 序列变异 系统发育 

分 类 号：R286.12[医药卫生—中药学]