Wei Xue-Ping, Li Hui-Juan, Che Peng, Guo Hao-Jie, Zhang Ben-Gang, Liu Hai-Tao, Qi Yao-Dong
Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
Chin Herb Med. 2020 Jun 22;12(3):247-256. doi: 10.1016/j.chmed.2019.09.009. eCollection 2020 Jul.
and are the two important medicinal plants that have long been used under the names of "Nan-Wuweizi" and "Wuweizi", respectively. The misuse of "Nan-Wuweizi" and "Wuweizi" in herbal medical products calls for an accurate method to distinguish these herbs. Chloroplast (cp) genomes have been widely used in species delimitation and phylogeny due to their uniparental inheritance and lower substitution rates than that of the nuclear genomes. To develop more efficient DNA markers for distinguishing , , and the related species, we sequenced the cp genome of and compared it to that of .
The cp genome of was sequenced at the Illumina HiSeq platform, and the reference-guided mapping of contigs was obtained with a assembly procedure. Then, comparative analyses of the cp genomes of and were carried out.
The cp genome of was 146 853 bp in length and consisted of a large single copy (LSC) region of 95 627 bp, a small single copy (SSC) region of 18 292 bp, and a pair of inverted repeats (IR) of 16 467 bp. GC content was 39.6%. A total of 126 functional genes were predicted, of which 113 genes were unique, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Five tRNA, four protein-coding genes, and all rRNA were duplicated in the IR regions. There were 18 intron-containing genes, including six tRNA genes and 12 protein-coding genes. In addition, 45 SSRs were detected. The whole cp genome of was 123 bp longer than that of . A total of 474 SNPs and 97 InDels were identified. Five genetic regions with high levels of variation (i > 0.015), S-G, A-D, I-S, T-D and F-32 were revealed.
We reported the cp genome of and revealed the SNPs and InDels between the cp genomes of and . This study shed light on the species identification and further phylogenetic study within the genus of .
[植物名称1]和[植物名称2]是两种重要的药用植物，长期以来分别以“南五味子”和“五味子”之名被使用。草药产品中“南五味子”和“五味子”的误用需要一种准确的方法来区分这些草药。叶绿体（cp）基因组因其单亲遗传以及比核基因组更低的替换率，已被广泛用于物种界定和系统发育研究。为开发更有效的DNA标记以区分[植物名称1]、[植物名称2]及相关物种，我们对[植物名称1]的叶绿体基因组进行了测序，并将其与[植物名称2]的叶绿体基因组进行比较。
在Illumina HiSeq平台对[植物名称1]的叶绿体基因组进行测序，并通过[拼接程序名称]获得重叠群的参考引导映射。然后，对[植物名称1]和[植物名称2]的叶绿体基因组进行比较分析。
[植物名称1]的叶绿体基因组长度为146853 bp，由一个95627 bp的大单拷贝（LSC）区域、一个18292 bp的小单拷贝（SSC）区域和一对16467 bp的反向重复序列（IR）组成。GC含量为39.6%。共预测到126个功能基因，其中113个基因是独特的，包括79个蛋白质编码基因、30个转运RNA（tRNA）基因和4个核糖体RNA（rRNA）基因。5个tRNA、4个蛋白质编码基因和所有rRNA在IR区域中是重复的。有18个含内含子的基因，包括6个tRNA基因和12个蛋白质编码基因。此外，检测到45个简单序列重复（SSR）。[植物名称1]的整个叶绿体基因组比[植物名称2]的长123 bp。共鉴定出474个单核苷酸多态性（SNP）和97个插入缺失（InDel）。揭示了5个高变异水平（i>0.015）的基因区域，即S-G、A-D、I-S、T-D和F-32。
我们报道了[植物名称1]的叶绿体基因组，并揭示了[植物名称1]和[植物名称2]叶绿体基因组之间的SNP和InDel。本研究为[植物名称所属属名]内的物种鉴定和进一步的系统发育研究提供了线索。
