Abstract: In order to clarify the phylogenetic relationship between the chloroplast genome characteristics of three medicinal plants, Panax japonicus var. major, P. japonicus var. bipinnatifidus, P. pseudoginseng var. elegantior in Qinba Mountains, we analysed the chloroplast genome characteristics and codon usage preferences by using bioinformatics techniques. The results were as follows:(1)The chloroplast genomes of three species of Panax were typical tetrad structure, the genome full size was between 156 071 to 156 104 bp, and the total GC-content was 38.10% with a high degree of genome size similarity.(2)A total of 133 coding genes were annotated, including 88 protein coding genes(PCGs), 37 tRNA genes, and 8 rRNA genes with a high degree of genome size similarity.(3)The chloroplast codon usage preferences of the three medicinal plants were comparable, with the third base of codon predominantly ending in A/U. Despite being affected by mutations, the codon usage patterns of the three medicinal plants were found to be mainly influenced by natural selection.(4)The phylogenetic results showed that the three Panax species were closely related, and P. pseudoginseng var. elegantior was more closely related to P. japonicus var. bipinnatifidus. In conclusion, this study presents a significant relationship between P. pseudoginseng var. elegantior and the original pharmacopeial plants of P. japonicus var. major. This finding has great importance for the development, utilization, and molecular identification of traditional Chinese medicinal material resources from P. japonicus var. major, and provides an important basis for further studies on the classification, phylogeny and evolutionary mechanisms of Panax species.

Key words: Panax japonicus var. major, P. japonicus var. bipinnatifidus, P. pseudoginseng var. elegantior, chloroplast genome, structural characteristics, codon preference

摘要： 为明确珠子参、羽叶三七和秀丽假人参3种药用植物叶绿体基因组特征与系统发育关系,该文以秦巴山区3种人参属药用植物为研究对象,运用生物信息学技术,分析其叶绿体基因组特征及密码子使用偏好性,并探讨三者之间的亲缘关系。结果表明:(1)3种人参属药用植物的叶绿体基因组为典型的四分体结构,序列全长为 156 071～156 104 bp,总 GC 含量为 38.10%,基因组大小相似度较高。(2)均注释到 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。(3)3种人参属药用植物叶绿体密码子使用偏好性相似,密码子第 3 位碱基以 A/U 结尾为主,密码子使用模式在受到突变影响的同时,主要受到自然选择的影响。(4)系统发育结果显示,3种人参属药用植物的亲缘关系较近,并且秀丽假人参同羽叶三七亲缘关系更近。综上认为,秀丽假人参与珠子参基源植物之间存在近缘关系,这项发现对于珠子参中药材的资源开发利用和分子鉴定,以及进一步研究人参属物种的分类、系统发育和进化机提供了重要依据。

关键词: 珠子参, 羽叶三七, 秀丽假人参, 叶绿体基因组, 结构特征, 密码子偏好性