Zhao Yongbing, Yin Jinlong, Guo Haiyan, Zhang Yuyu, Xiao Wen, Sun Chen, Wu Jiayan, Qu Xiaobo, Yu Jun, Wang Xumin, Xiao Jingfa
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; University of Chinese Academy of Sciences Beijing, China.
School of Pharmaceutical Sciences, Changchun University of Chinese Medicine Changchun, China.
Front Plant Sci. 2015 Jan 14;5:696. doi: 10.3389/fpls.2014.00696. eCollection 2014.
Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chinese P. ginseng strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS), and Yeshanshen (YSS). The total chloroplast genome sequence length for DMY, EMY, and GLS was 156,354 bp, while that for YSS was 156,355 bp. Comparative genomic analysis of the chloroplast genome sequences indicate that gene content, GC content, and gene order in DMY are quite similar to its relative species, and nucleotide sequence diversity of inverted repeat region (IR) is lower than that of its counterparts, large single copy region (LSC) and small single copy region (SSC). A comparison among these four P. ginseng strains revealed that the chloroplast genome sequences of DMY, EMY, and GLS were identical and YSS had a 1-bp insertion at base 5472. To further study the heterogeneity in chloroplast genome during domestication, high-resolution reads were mapped to the genome sequences to investigate the differences at the minor allele level; 208 minor allele sites with minor allele frequencies (MAF) of ≥0.05 were identified. The polymorphism site numbers per kb of chloroplast genome sequence for DMY, EMY, GLS, and YSS were 0.74, 0.59, 0.97, and 1.23, respectively. All the minor allele sites located in LSC and IR regions, and the four strains showed the same variation types (substitution base or indel) at all identified polymorphism sites. Comparison results of heterogeneity in the chloroplast genome sequences showed that the minor allele sites on the chloroplast genome were undergoing purifying selection to adapt to changing environment during domestication process. A study of P. ginseng chloroplast genome with particular focus on minor allele sites would aid in investigating the dynamics on the chloroplast genomes and different P. ginseng strains typing.
人参（Panax ginseng C.A. Meyer）是一种重要的药用植物，常用于传统中药。利用下一代测序（NGS）技术，我们测定了4个人参中国菌株的叶绿体全基因组序列，分别是大马牙（DMY）、二马牙（EMY）、高丽参（GLS）和野山参（YSS）。DMY、EMY和GLS的叶绿体全基因组序列长度为156,354 bp，而YSS的为156,355 bp。叶绿体基因组序列的比较基因组分析表明，DMY的基因含量、GC含量和基因顺序与其近缘物种非常相似，反向重复区域（IR）的核苷酸序列多样性低于其对应区域，即大单拷贝区域（LSC）和小单拷贝区域（SSC）。这4个人参菌株之间的比较显示，DMY、EMY和GLS的叶绿体基因组序列相同，而YSS在第5472个碱基处有一个1-bp的插入。为了进一步研究驯化过程中叶绿体基因组的异质性，将高分辨率读数映射到基因组序列上，以研究次要等位基因水平的差异；共鉴定出208个次要等位基因位点，其次要等位基因频率（MAF）≥0.05。DMY、EMY、GLS和YSS的叶绿体基因组序列每kb的多态性位点数量分别为0.74、0.59、0.97和1.23。所有次要等位基因位点均位于LSC和IR区域，并且这4个菌株在所有鉴定出的多态性位点上表现出相同的变异类型（替换碱基或插入缺失）。叶绿体基因组序列异质性的比较结果表明，驯化过程中叶绿体基因组上的次要等位基因位点正在经历纯化选择以适应不断变化的环境。一项特别关注次要等位基因位点的人参叶绿体基因组研究将有助于研究叶绿体基因组的动态变化以及不同人参菌株的分型。
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