Phylogenomics and Genetic Diversity of and Its Allies (, Boraginaceae) in China.

is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of in China, and the two species and are the source plants of 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 species using genome skimming methods. The chloroplast genomes exhibited quadripartite structures with lengths from 149,539 and 152,040 bp. Three variable markers (, , and ) were identified, and these markers exhibited more variable sites than universal chloroplast markers. The phylogenetic relationships among the five species were completely resolved using the whole chloroplast genome sequences. 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 and have high levels of genetic diversity and comprise two and three subclades, respectively. The two clades of exhibited significant genetic differences and diverged at 10.18 Ma in the middle Miocene. Three clades of diverged in the Pleistocene. The results provided new insight into evolutionary history of species and promoted the conservation and exploitation of and