Li Dong-Mei, Zhu Gen-Fa, Xu Ye-Chun, Ye Yuan-Jun, Liu Jin-Mei
Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Plants (Basel). 2020 Feb 24;9(2):286. doi: 10.3390/plants9020286.
(), () and (), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and phylogenetic analysis. Here, we sequenced three complete chloroplast genomes of , sampled from Guangdong and , and analyzed the published chloroplast genomes of () and sampled from Hainan to retrieve useful chloroplast molecular resources for . The five chloroplast genomes possessed typical quadripartite structures comprising of a large single copy (LSC, 87,248-87,667 bp), a small single copy (SSC, 15,306-18,295 bp) and a pair of inverted repeats (IR, 26,917-29,707 bp). They had similar gene contents, gene orders and GC contents, but were slightly different in the numbers of small sequence repeats (SSRs) and long repeats. Interestingly, fifteen highly divergent regions (, , , , , , , , , , , , , , and ), which could be suitable for species identification and phylogenetic studies, were detected in the chloroplast genomes. Comparative analyses among the five chloroplast genomes indicated that 1891 mutational events, including 304 single nucleotide polymorphisms (SNPs) and 118 insertion/deletions (indels) between and , 367 SNPs and 122 indels between and sampled from Guangdong, 331 SNPs and 115 indels between and , 371 SNPs and 120 indels between and sampled from Hainan, and 20 SNPs and 23 indels between the two accessions of , were accurately located. Additionally, phylogenetic relationships based on SNP matrix among 28 whole chloroplast genomes showed that was a sister branch to in the family Zingiberaceae, and that the five accessions were divided into three groups, one including , another including and , and the other including two accessions of . In conclusion, the complete chloroplast genomes of the three medicinal species in this study provided valuable genomic resources for further phylogeny and species identification in the family Zingiberaceae.
属于姜科的（）、（）和（）具有多种药用特性。非模式植物的叶绿体基因组为物种鉴定和系统发育分析提供了有价值的信息。在此，我们对从广东采集的（）、（）以及从海南采集的（）的三个完整叶绿体基因组进行了测序，并分析了已发表的（）和从海南采集的（）的叶绿体基因组，以获取用于（）的有用叶绿体分子资源。这五个（）叶绿体基因组具有典型的四分体结构，包括一个大单拷贝（LSC，87,248 - 87,667 bp）、一个小单拷贝（SSC，15,306 - 18,295 bp）和一对反向重复序列（IR，26,917 - 29,707 bp）。它们具有相似的基因含量、基因顺序和GC含量，但在小序列重复（SSR）和长重复序列的数量上略有不同。有趣的是，在（）叶绿体基因组中检测到15个高度分化的区域（，，，，，，，，，，，，，，和），这些区域可用于物种鉴定和系统发育研究。五个叶绿体基因组之间的比较分析表明，准确定位了1891个突变事件，包括（）和（）之间的304个单核苷酸多态性（SNP）和118个插入/缺失（indel）、从广东采集的（）和（）之间的367个SNP和122个indel、（）和（）之间的331个SNP和115个indel、从海南采集的（）和（）之间的371个SNP和120个indel，以及两个（）种质之间的20个SNP和23个indel。此外，基于28个完整叶绿体基因组的SNP矩阵的系统发育关系表明，（）在姜科中是（）的姐妹分支，并且这五个（）种质分为三组，一组包括（），另一组包括（）和（），另一组包括两个（）种质。总之，本研究中三种药用（）物种的完整叶绿体基因组为姜科进一步的系统发育和物种鉴定提供了有价值的基因组资源。
