Table_1_Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China.docx

Arnebiae Radix is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of Arnebia in China, and the two species Arnebia euchroma and Arnebia guttata are the source plants of Arnebiae Radix according to the Chinese Pharmacopoeia. Molecular markers that permit species identification and facilitate studies of the genetic diversity and divergence of the wild populations of these two source plants have not yet been developed. Here, we sequenced the chloroplast genomes of 56 samples of five Arnebia species using genome skimming methods. The Arnebia chloroplast genomes exhibited quadripartite structures with lengths from 149,539 and 152,040 bp. Three variable markers (rps16-trnQ, ndhF-rpl32, and ycf1b) were identified, and these markers exhibited more variable sites than universal chloroplast markers. The phylogenetic relationships among the five Arnebia species were completely resolved using the whole chloroplast genome sequences. Arnebia arose during the Oligocene and diversified in the middle Miocene; this coincided with two geological events during the late Oligocene and early Miocene: warming and the progressive uplift of Tianshan and the Himalayas. Our analyses revealed that A. euchroma and A. guttata have high levels of genetic diversity and comprise two and three subclades, respectively. The two clades of A. euchroma exhibited significant genetic differences and diverged at 10.18 Ma in the middle Miocene. Three clades of A. guttata diverged in the Pleistocene. The results provided new insight into evolutionary history of Arnebia species and promoted the conservation and exploitation of A. euchroma and A. guttata.

软紫草（Arnebiae Radix）是一种具有多效活性的传统中药材，已有数百年的应用历史。中国境内分布有5种紫草属（Arnebia）植物，根据《中华人民共和国药典》，新疆紫草（Arnebia euchroma）与斑花紫草（Arnebia guttata）是软紫草（Arnebiae Radix）的基原植物。目前尚未开发出可用于这两种基原植物野生种群的物种鉴定、遗传多样性及遗传分化研究的分子标记。本研究采用基因组浅层测序（genome skimming）技术，对5个紫草属物种的56份样本的叶绿体基因组（chloroplast genomes）进行了测序。紫草属植物的叶绿体基因组均呈现四分体结构，基因组长度介于149539 bp至152040 bp之间。本研究筛选得到3个高变分子标记（rps16-trnQ、ndhF-rpl32及ycf1b），相较于通用叶绿体标记，这些标记拥有更多的变异位点。基于完整叶绿体基因组序列，本研究完全解析了5个紫草属物种间的系统发育关系。紫草属起源于渐新世（Oligocene），并于中新世（Miocene）中期发生分化；这一演化时间与渐新世晚期至中新世早期的两次地质事件相吻合：全球气候变暖以及天山（Tianshan）与喜马拉雅山脉（Himalayas）的阶段性隆升。分析结果显示，新疆紫草（A. euchroma）与斑花紫草（A. guttata）均具有较高的遗传多样性，二者分别可划分为2个和3个亚支。新疆紫草的两个进化支存在显著的遗传分化，其分化时间为中新世中期的10.18 Ma（百万年）。斑花紫草的3个进化支则于更新世（Pleistocene）发生分化。本研究结果为紫草属植物的演化历史提供了新的认知，并为新疆紫草与斑花紫草的保护与开发利用提供了理论支撑。