药学学报, 2021, 56(2): 618-629
引用本文:
张明英, 张雨曲, 李依民, 高静, 沈霞, 杨新杰, 颜永刚, 王昌利, 张岗. 北柴胡、紫花阔叶柴胡叶绿体全基因组解析及柴胡属药用植物叶绿体基因组比较与系统发育分析[J]. 药学学报, 2021, 56(2): 618-629.
ZHANG Ming-ying, ZHANG Yu-qu, LI Yi-min, GAO Jing, SHEN Xia, YANG Xin-jie, YAN Yong-gang, WANG Chang-li, ZHANG Gang. Complete plastid genomes of Bupleurum chinense DC. and B. boissieuanum H. Wolff, with comparative and phylogenetic analyses of medicinal Bupleurum species[J]. Acta Pharmaceutica Sinica, 2021, 56(2): 618-629.

北柴胡、紫花阔叶柴胡叶绿体全基因组解析及柴胡属药用植物叶绿体基因组比较与系统发育分析
张明英, 张雨曲, 李依民, 高静, 沈霞, 杨新杰, 颜永刚, 王昌利, 张岗
陕西中医药大学药学院/陕西省秦岭中草药应用开发工程技术研究中心, 陕西 西安 712046
摘要:
柴胡属(Bupleurum L.)是伞形科(Apiaceae)中具有重要经济价值的药用类群。本研究利用Illumina HiSeq X Ten平台测序获得北柴胡(B.chinense DC.)和紫花阔叶柴胡(B.boissieuanum H.Wolff)的叶绿体全基因组序列,对其进行了组装、注释和特征分析,并与同属已发表的叶绿体全基因组进行了比较和系统发育分析。北柴胡和紫花阔叶柴胡叶绿体全基因组大小分别为155 458、155 800 bp,均为由一个大单拷贝区(large single copy,LSC;85 343、85 804 bp)、一个小单拷贝区(small single copy,SSC;17 495、17 410 bp)和一对反向重复区(inverted repeat,IRa/IRb;26 310、26 293 bp)构成的环状四分体结构;两者分别注释得到129个基因,包括84个蛋白编码基因、37个tRNA基因和8个rRNA基因;此外,两者重复序列的类型与分布模式相似,但数量有所差异。比较基因组学分析结果表明,柴胡属植物叶绿体全基因组大小、结构、GC含量及基因组成和排列顺序等在种内、种间均高度保守,IRs区未出现明显扩张或收缩;序列的种间变异高于种内,非编码序列(包括基因间区和内含子)变异高于编码基因序列,LSC和SSC区序列变异高于IRs区;此外,筛选到11条核苷酸多样性较高的种间高变异序列,分别位于LSC和SSC区。系统发育分析结果强烈支持柴胡属为单系,其中,北柴胡同种不同个体聚为一支,并与紫花鸭跖柴胡(B.commelynoideum H.Boissieu)亲缘关系最近,而紫花阔叶柴胡与三岛柴胡(B.falcatum L.)亲缘关系更近。本研究将为柴胡属药用植物的分类鉴定、系统发育及资源开发利用等相关研究提供基础。
关键词:    柴胡属      叶绿体基因组      简单重复序列      序列变异      系统发育     
Complete plastid genomes of Bupleurum chinense DC. and B. boissieuanum H. Wolff, with comparative and phylogenetic analyses of medicinal Bupleurum species
ZHANG Ming-ying, ZHANG Yu-qu, LI Yi-min, GAO Jing, SHEN Xia, YANG Xin-jie, YAN Yong-gang, WANG Chang-li, ZHANG Gang
College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xi'an 712046, China
Abstract:
Bupleurum L. (Apiaceae) is an economically important genus, in which many species are of medicinal value. In this study, the complete plastid genomes (plastomes) of B. chinense DC. and B. boissieuanum H. Wolff were sequenced and their characteristics were investigated. Comparative and phylogenetic analyses were conducted with other published Bupleurum plastomes. The complete plastomes of B. chinense and B. boissieuanum were 155 458 and 155 800 bp in length, and both exhibited the typical quadripartite circular structure consisting of a large single copy region (LSC, 85 343 and 85 804 bp), a small single copy region (SSC, 17 495 and 17 410 bp), and a pair of inverted repeat regions (IRa/b, 26 310 and 26 293 bp), respectively. A total of 129 genes, including 84 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes were identified from each of the two plastomes. Repeat sequences detected were similar in types and distribution patterns, but the numbers were slightly different. Comparative analyses revealed that the Bupleurum plastomes were highly conserved in length, structure, the guanine and cytosine (GC) content, and gene content and order, both intraspecifically and interspecifically, and no obvious expansion or contraction of the inverted repeat regions occurred. Sequence variation was lower within the same species than among different species, noncoding sequences (including intergenic regions and introns) showed a higher divergence than the protein-coding sequences, and sequences in the LSC and SSC regions were more divergent than those in the IR regions. In addition, 11 sequences with higher nucleotide diversity among species were detected in the LSC and SSC regions. All studied Bupleurum species were inferred forming a monophyletic group with a 100% bootstrap value. Bupleurum chinense and B. boissieuanum were phylogenetically closest to B. commelynoideum and B. falcatum, separately, with all three B. chinense accessions clustered into a distinct clade. These results provide genetic information for further species identification, phylogenetic resolution, and will assist in exploration and utilization of medicinal Bupleurum species.
Key words:    Bupleurum    plastid genome    simple sequence repeat    sequence divergence    phylogeny   
收稿日期: 2020-08-28
DOI: 10.16438/j.0513-4870.2020-1419
基金项目: 陕西省自然科学基础研究计划(2019JQ-876);陕西中医药大学校级科研课题(2020GP34);陕西中医药大学博士科研启动经费(104080001);陕西中医药大学思邈人才工程(141306200105);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);2019年医疗服务与保障能力提升补助资金项目(中医药事业传承与发展部分第四次全国中药资源普查项目)(财社[2019]39号);陕西省高校青年杰出人才支持计划项目.
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Email: jay_gumling2003@aliyun.com
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