Complete chloroplast genome sequence of Epimedium shuichengense S. Z. He (Berberidaceae), an endangered species endemic to China

Abstract Epimedium shuichengense S. Z. He is a rare and endangered species endemic to Guizhou, China. In this study, the complete chloroplast (cp) genome of E. shuichengense was sequenced. The total cp genomes size was 157,046 bp in length, with 38.8% of GC content, including four distinct regions: the large single-copy region (LSC, 88,394 bp), small single-copy region (SSC, 17,048 bp), and a pair of inverted repeat regions (IRs, each for 20,820 bp). The whole cp genome of E. shuichengense encoded 130 unique genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with the previously reported cp genomes showed that all the samples of Epimedium are grouped into one group, which can be easily separated from out groups, and E. shuichengense with E. borealiguizhouense into a supported branch.

Epimdium L. is the largest perennial herbaceous genus, which belongs to Beiberdaceae (Ranales), and famous for its medicinal value. To date, the genus comprises about 65 species, of which about 56 species are distributed in China (Ying et al. 2000;He 2014;Xu et al. 2019). Epimedii folium has the therapeutic effects of nourishing kidney, strengthening bones and reliev-ing rheumatism, and has a long history of medical use intraditional Chinese medicine (TCM) (Wu et al. 2010;Ma et al. 2011;Jiang et al. 2016). In recent years, the research on Epimedium family has attracted more attention.
Epimdium shuichengense, a rare and endangered species endemic to GuiZhou, China, is a new species discovered by Professor S. Z. He in 1996, and only distributed in a small area in the Shuicheng county of Guizhou, China, with a very small population and urgently needs to be protected (Wang et al. 2009). In this study, we sequenced the cp genomes of E. shuichengense, aiming to provide valuable genetic information for the study of evolutionary dynamics and conservation.
In present study, the fresh young leaves of E. shuichengense were collected from the Shuicheng county, Guizhou Province, China, (N 26 37 0 26.74 00 , E 104 44 0 33.13 00 ), and a voucher specimen (with collection numbers of YFL_20180326) has been deposited in the Herbarium of Guizhou University of Traditional Chinese Medicine (GZYGH), Guizhou, China. Total DNA was extracted from the fresh leaves of E. shuichengense by modified CTAB method (Doyle and Doyle 1987). Sequencing was carried out on the Illumina HiSeq X-Ten to generate approximately 5-70 million paired-end 150 bp reads at Beijing Genomics Institute (BGI, Wuhan, China). The filtered reads were assembled into a complete cp genome by the program GetOrganelle v 1.5 (Jin et al. 2018), in this pipeline, the complete cp genome reads were extracted from total genomic reads and were subsequently assembled using SPAdes version 3.10 (Bankevich et al. 2012). The genes were annotated using PGA (Qu et al. 2019) and Geneious 11.0.3 (Kearse et al. 2012) with the published complete cp genome of E. lishihchenii ( GenBank accession number: NC_029944) as the reference. Transfer RNAs (tRNAs) were confirmed by their specific structure predicted by tRNAscan-SE 2.0 (Lowe and Chan 2016).
In order to explore the phylogenetic relationship of E. shuichengense, we downloaded the whole cp genomes of 17 species from the NCBI GenBank database. Maximum likelihood (ML) analyses were performed using RAxML software (Stamatakis 2014).
The phylogenetic analysis was carried out using the complete cp genome sequences of E. shuichengense, 15 reported Epimedium species, Nandina and Berberis of Berberidaceae as outgroup (Figure 1). The results showed that all the 15 species of the Epimedium, endemic to China, clustered into a supported branch and were separated from E. koreanmum distributed in Korea. Epimedium shuichengense with E. borealiguizhouense into a supported branch. The phylogenetic relationships of 16 species of Epimedium based on the cp genome data were not closely related to floral characters. This cp genome is the first report for the E. shuichengense and will be useful data for developing markers for further studies on resolving the relationship within the Epimedium.

Disclosure statement
No potential conflict of interest was reported by the author(s).