Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China.
Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
Molecules. 2017 Nov 1;22(11):1875. doi: 10.3390/molecules22111875.
Amomum kravanh is an important edible and medicinal herb, the dried fruits of which are widely used in traditional herbal medicine as cardamom. We sequenced and analyzed the complete chloroplast (cp) genome of A. kravanh with herbgenomics technologies. The size of the A. kravanh cp genome was 162,766 bp, which consisted of long (LSC; 87,728 bp) and short (SSC; 15,390 bp) single-copy regions, separated by a pair of inverted repeats (IRs; 29,824 bp). The genome encoded 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. A total of 299 simple sequence repeats (SSRs) were identified in the A. kravanh cp genome, which provides an effective method to study species identification and population genetics of the medicinal plant. Moreover, one complement, 12 forward, 12 palindrome and two reverse repeats were detected. Comparative cp genome sequence analysis of four Zingiberaceae species indicated that their intergenic spacers are highly divergent, although the gene order, gene content and genome structure differed only minimally. In particular, there was a remarkable expansion of the IR regions in the A. kravanh cp genome. Phylogenetic analysis strongly supported a sister relationship between A. kravanh and Alpinia zerumbet. This study identified the unique characteristics of the A. kravanh cp genome and might provide valuable information for future studies aiming for Amomum identification, and provide insights into the taxonomy of the commelinids.
阳春砂是一种重要的食用和药用植物，其干燥果实被广泛用作传统草药中的小豆蔻。我们使用草药基因组学技术对阳春砂的完整叶绿体（cp）基因组进行了测序和分析。阳春砂 cp 基因组大小为 162766bp，由长（LSC；87728bp）和短（SSC；15390bp）单拷贝区域组成，由一对反向重复（IRs；29824bp）隔开。该基因组编码 114 个独特基因，包括 80 个蛋白质编码基因、30 个 tRNA 和 4 个 rRNA。在阳春砂 cp 基因组中鉴定出 299 个简单序列重复（SSR），为研究药用植物的物种鉴定和群体遗传学提供了有效的方法。此外，还检测到一个互补序列、12 个正向重复序列、12 个回文重复序列和两个反向重复序列。对四种姜科物种的 cp 基因组序列比较分析表明，尽管基因顺序、基因含量和基因组结构仅略有差异，但它们的基因间区高度分化。特别是，阳春砂 cp 基因组的 IR 区显著扩张。系统发育分析强烈支持阳春砂与艳山姜之间的姐妹关系。本研究确定了阳春砂 cp 基因组的独特特征，可为今后的 Amomum 鉴定研究提供有价值的信息，并为 commelinids 的分类学研究提供了新的见解。
