Wu Liwei, Nie Liping, Xu Zhichao, Li Pei, Wang Yu, He Chunnian, Song Jingyuan, Yao Hui
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 and Peking Union Medical College, Beijing, China.
Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China.
Front Genet. 2020 Sep 18;11:980. doi: 10.3389/fgene.2020.00980. eCollection 2020.
Analysis of the relationships among wild species of section in the plant genus has traditionally been problematic. Interspecies relationships cannot be effectively determined using phenotypic traits alone or through analysis of nuclear or chloroplast DNA fragments. Elucidation of complete chloroplast genome sequences will aid the identification and phylogeny of these species. In this study, the complete chloroplast genomes of three sect. plants were sequenced and analyzed. Comparative and phylogenetic analyses of the complete chloroplast genomes of all eight species of sect. were then conducted. The three complete chloroplast genomes gained in this study showed four-part annular structures, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. There was greater variation in the noncoding regions of the sequences than in the conserved protein-coding regions. Sequence variations in the small single copy (SSC) regions and large single copy (LSC) regions were considerably greater than those in the inverted repeat (IR) regions. Phylogenetic analysis revealed that the species of sect. clustered in one branch and then subdivided into smaller branches. As for the three complete chloroplast genome sequences obtained in this study, clustered with another sequence from the GenBank database, clustered with , and var. clustered with . It was also found that the complete chloroplast genomes, LSC regions, and SSC regions all showed great abilities in identification and phylogenetic analysis of the species of sect. , while IRs regions and highly variable regions were not suitable for the species of sect. .
对植物属中某组野生种之间关系的分析传统上一直存在问题。仅使用表型特征或通过分析核DNA或叶绿体DNA片段无法有效确定种间关系。完整叶绿体基因组序列的阐明将有助于这些物种的鉴定和系统发育研究。在本研究中，对三种某组植物的完整叶绿体基因组进行了测序和分析。然后对该组所有八个物种的完整叶绿体基因组进行了比较和系统发育分析。本研究获得的三个完整叶绿体基因组呈现出四分环状结构，并且基因组长度、结构、GC含量、密码子使用和基因分布高度相似。序列的非编码区比保守的蛋白质编码区有更大的变异。小单拷贝（SSC）区域和大单拷贝（LSC）区域的序列变异明显大于反向重复（IR）区域。系统发育分析表明，该组物种聚集在一个分支中，然后再细分为较小的分支。至于本研究获得的三个完整叶绿体基因组序列，[物种名称1]与来自GenBank数据库的另一个[物种名称2]序列聚类，[物种名称3]与[物种名称4]聚类，[物种名称5]变种与[物种名称6]聚类。还发现完整叶绿体基因组、LSC区域和SSC区域在该组物种的鉴定和系统发育分析中均表现出很强的能力，而IR区域和高变区域不适用于该组物种。
