Zhang Zhi-Fei, Zhao Zhong-Zhen, Wang Xin, Yin Guang-Yao, Chen Ying, Man Jin-Hui, Shi Yue, Huang Yu-Ying, Liu Shan-Hu, Liu Zi-Qi, Wang Xiao-Hui, Wei Sheng-Li
School of Chinese Materia Medica, Beijing University of Chinese Medicine Beijing 102488, China.
Heilongjiang Beicaotang Traditional Chinese Medicine Co., Ltd. Harbin 150900, China.
Zhongguo Zhong Yao Za Zhi. 2023 Mar;48(5):1229-1237. doi: 10.19540/j.cnki.cjcmm.20221208.101.
Eleutherococcus senticosus is one of the Dao-di herbs in northeast China. In this study, the chloroplast genomes of three E. senticosus samples from different genuine producing areas were sequenced and then used for the screening of specific DNA barcodes. The germplasm resources and genetic diversity of E. senticosus were analyzed basing on the specific DNA barcodes. The chloroplast genomes of E. senticosus from different genuine producing areas showed the total length of 156 779-156 781 bp and a typical tetrad structure. Each of the chloroplast genomes carried 132 genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes were relatively conserved. Sequence analysis of the three chloroplast genomes indicated that atpI, ndhA, ycf1, atpB-rbcL, ndhF-rpl32, petA-psbJ, psbM-psbD, and rps16-psbK can be used as specific DNA barcodes of E. senticosus. In this study, we selected atpI and atpB-rbcL which were 700-800 bp and easy to be amplified for the identification of 184 E. senticosus samples from 13 genuine producing areas. The results demonstrated that 9 and 10 genotypes were identified based on atpI and atpB-rbcL sequences, respectively. Furthermore, the two barcodes identified 23 genotypes which were named H1-H23. The haplotype with the highest proportion and widest distribution was H10, followed by H2. The haplotype diversity and nucleotide diversity were 0.94 and 1.82×10~(-3), respectively, suggesting the high genetic diversity of E. senticosus. The results of the median-joining network analysis showed that the 23 genotypes could be classified into 4 categories. H2 was the oldest haplotype, and it served as the center of the network characterized by starlike radiation, which suggested that population expansion of E. senticosus occurred in the genuine producing areas. This study lays a foundation for the research on the genetic quality and chloroplast genetic engineering of E. senticosus and further research on the genetic mechanism of its population, providing new ideas for studying the genetic evolution of E. senticosus.
刺五加是中国东北地区的道地药材之一。在本研究中，对来自不同道地产区的3份刺五加样本的叶绿体基因组进行测序，然后用于筛选特异性DNA条形码。基于特异性DNA条形码分析刺五加的种质资源和遗传多样性。来自不同道地产区的刺五加叶绿体基因组全长为156 779 - 156 781 bp，具有典型的四分体结构。每个叶绿体基因组携带132个基因，包括87个蛋白质编码基因、37个tRNA和8个rRNA。叶绿体基因组相对保守。对3个叶绿体基因组的序列分析表明，atpI、ndhA、ycf1、atpB - rbcL、ndhF - rpl32、petA - psbJ、psbM - psbD和rps16 - psbK可作为刺五加的特异性DNA条形码。在本研究中，我们选择了长度为700 - 800 bp且易于扩增的atpI和atpB - rbcL用于鉴定来自13个道地产区的184份刺五加样本。结果表明，基于atpI和atpB - rbcL序列分别鉴定出9种和10种基因型。此外，这两个条形码鉴定出23种基因型，命名为H1 - H23。比例最高、分布最广的单倍型是H10，其次是H2。单倍型多样性和核苷酸多样性分别为0.94和1.82×10⁻³，表明刺五加具有较高的遗传多样性。中介连接网络分析结果表明，23种基因型可分为4类。H2是最古老的单倍型，它作为网络中心呈星状辐射，这表明刺五加在道地产区发生了种群扩张。本研究为刺五加的遗传品质和叶绿体基因工程研究以及其种群遗传机制的进一步研究奠定了基础，为刺五加遗传进化研究提供了新思路。
