Complete chloroplast genomes of 6 rare and endangered species of Epimedium (Berberidaceae) from China: Genomic features, comparative analysis, and phylogenetic relationship

Abstract

Epimedium, as the Traditional Chinese Medicine (TCM) for more than 2,000 years, numerous species are widely used for their medicinal and ornamental values in China. However, the effective conservation of the Epimedium is faced with many challenges due to habitat loss caused by over harvesting. Currently, most Epimedium species are listed as endangered by the International Union for Conservation of Nature (IUCN). In this study, we utilized second-generation sequencing technology to compare the chloroplast (cp) genome structures of six rare and endangered species of Epimedium from China. The chloroplast genomes of the six species follow a typical quadripartite structure. The length of cp genomes ranged from 157,046 bp to 164,962 bp, with a total of 129–139 annotated genes, including 84–94 protein-coding genes, 7–8 rRNA genes, and 37 tRNA genes. The study also detected 34–36 tandem repeat sequences, 64–74 SSR sequences, 29–32 high-frequency codons, and 4 highly variable regions. Phylogenetic analysis supports the monophyly of Epimedium. Based on molecular clock analyses, the species within Epimedium are hypothesized to have occurred approximately 144 million years ago during the Pliocene. This study enriches the chloroplast genome data of the endangered species Epimedium, which not only provides a basic basis for its classification, identification and phylogeny, but also provides an important information for its resource development and conservation.