Zhang Cai-Yun, Liu Tong-Jian, Mo Xiao-Lu, Huang Hui-Run, Yao Gang, Li Jian-Rong, Ge Xue-Jun, Yan Hai-Fei
Guangdong Food and Drug Vocational College, Guangzhou 510520, China.
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Plants (Basel). 2020 Nov 5;9(11):1497. doi: 10.3390/plants9111497.
Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of , especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Desf., C. Y. Wu et Y. C. Huang, and two cultivars of (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of (Makino) Press and (Lour.) Kuntze) suggested that cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity () value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and For the overall mean substitution rates, the synonymous () and nonsynonymous () substitution rate values of protein-coding genes varied approximately threefold, while the values among different functional gene groups showed a wider variation range. Overall, the cp genomes of will be useful for phylogenetic reconstruction, species delimitation and identification in the future.
广藿香属（唇形科刺蕊草族中最大的属）约有80个物种，主要分布于南亚、东南亚至中国。该属包含许多广藿香植物，它们具有重要的经济价值，但在分类学上存在困难。因此，有必要对更多叶绿体（cp）基因组进行表征，以用于该属的系统发育分析和物种鉴定，特别是对于广藿香植物。在本研究中，我们新生成了三种广藿香植物（即广藿香、海南广藿香和两个广藿香（布兰科）栽培品种）的四个cp基因组。对所有样本（包括在线可得的刺蕊草和罗勒的cp基因组）的比较表明，广藿香属的cp基因组在基因组大小和基因含量方面高度保守，具有典型的四分体环状结构。尽管通过逐步窗口分析确定了七个差异热点区域，但cp基因组的种间差异一直保持在相对较低的水平。核苷酸多样性（）值与间隙比例（插入缺失）显著相关，但与GC含量显著负相关。我们基于80个蛋白质编码基因的系统发育分析为唇形科和广藿香属产生了高分辨率的主干拓扑结构。对于总体平均替换率，蛋白质编码基因的同义（）和非同义（）替换率值大约相差三倍，而不同功能基因组之间的值显示出更宽的变化范围。总体而言，广藿香属的cp基因组将有助于未来的系统发育重建、物种界定和鉴定。
