Comparative and phylogenetic analyses of Swertia L. (Gentianaceae) medicinal plants (from Qinghai, China) based on complete chloroplast genomes

Abstract Swertia L. is a large genus in Swertiinae (Gentianaceae). In China, many Swertia species are used as traditional Tibetan medicines, known as “Zangyinchen” or “Dida”. However, the phylogenetic relationships among Swertia medicinal plants and their wild relatives have remained unclear. In this study, we sequenced and assembled 16 complete chloroplast (cp) genomes of 10 Swertia species, mainly distributed in Qinghai Province, China. The results showed that these species have typical structures and characteristics of plant cp genomes. The sizes of Swertia cp genomes are ranging from 149,488 bp to 154,097 bp. Most Swertia cp genomes presented 134 genes, including 85 protein coding genes, eight rRNA genes, 37 tRNA genes, and four pseudogenes. Furthermore, the GC contents and boundaries of cp genomes are similar among Swertia species. The phylogenetic analyses indicated that Swertia is a complex polyphyletic group. In addition, positive selection was found in psaI and petL genes, indicating the possible adaptation of Qinghai Swertia species to the light environment of the Qinghai-Tibet plateau. These new cp genome data could be further investigated to develop DNA barcodes for Swertia medicinal plants and for additional systematic studies of Swertia and Swertiinae species.

獐牙菜属（Swertia L.）是龙胆亚族（Swertiinae，龙胆科Gentianaceae）下的一个大属。在我国，多种獐牙菜属植物被用作传统藏药，习称“藏茵陈”或“蒂达”。然而，目前獐牙菜属药用植物与其野生近缘类群间的系统发育关系仍未明确。本研究对10种主要分布于中国青海省的獐牙菜属植物的16个完整叶绿体（chloroplast，cp）基因组进行了测序与组装。结果显示，这些物种的叶绿体基因组具备典型的植物叶绿体基因组结构与特征。獐牙菜属叶绿体基因组的长度介于149488 bp至154097 bp之间。多数獐牙菜属叶绿体基因组包含134个基因，其中包括85个蛋白编码基因、8个核糖体RNA（ribosomal RNA，rRNA）基因、37个转运RNA（transfer RNA，tRNA）基因以及4个假基因。此外，獐牙菜属物种间的叶绿体基因组GC含量与边界区域特征较为相似。系统发育分析表明，獐牙菜属是一个复杂的多系类群。此外，研究在psaI与petL基因中检测到正选择信号，表明分布于青海的獐牙菜属物种可能已适应青藏高原的光照环境。本研究新增的叶绿体基因组数据，可进一步用于开发獐牙菜属药用植物的DNA条形码，以及开展獐牙菜属与龙胆亚族物种的更多系统学研究。