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. 2020 Jan 24;5(1):817–818. doi: 10.1080/23802359.2020.1715877

The complete chloroplast genome of Epimedium wushanense T. S. Ying. (Berberidaceae), a traditional Chinese medicinal herb

Ting Liu a,b,*, Xiang Liu b,c,*, Yanjiao Luo b,d, Yu Yao b, Chunmei Wen b,e, Qianru Yang b, Guoan Shen b,✉, Baolin Guo b,✉
PMCID: PMC7748643  PMID: 33366765

Abstract

Epimedium wushanense is a well-known medicinal plant in Berberidaceae in China. In this study, we sequenced the complete chloroplast (cp) genome of E. wushanense. The results showed that the cp genome of E. wushanense was 157,283 bp in length, which is composed of a large single-copy region (LSC, 88,579 bp) and a small single-copy region (SSC, 17,082 bp) that were separated by a pair of inverted repeat regions (IRa and IRb, 25,811 bp). The chloroplast genome of E. wushanense contains 112 unique genes, of which are 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content was 38.78%. The phylogenetic tree analysis showed that E. wushanense was closely related to E. pseudowushanense, E. lishihchenii, and E. sagittatum.

Keywords: Chloroplast genome, Epimedium wushanense, Berberidaceae

Epimedium wushanense is a well-known medicinal plant in Berberidaceae in China. The leaves of E. wushanense have been officially adopted in the Chinese Pharmacopoeia Commission (2015) under the crude drug names of “Wushan Yinyanghuo” in Chinese. Epimedii Folium has the therapeutic functions of strengthening muscles and bones, dispelling wind dampness and so on. In recent years, with the deepening of the research on the extract of Epimedii Folium, it has been found that Epimedii Folium has more effects on human health, such as treating osteoporosis, improving immunity and anti-aging. In addition, Epimedii Folium extract has also been widely used in cosmetics and health products. For a long time, E. wushanense mostly relies on wild harvested resources (Ma et al. 2011; Tong et al. 2013). However, it is hard to clearly distinguish E. wushanense from other closely related species in the Epimedium family. Herein, we reported the complete chloroplast (cp) genome sequence of E. wushanense and revealed its phylogenetic relationships with related species in the Berberidaceae.

In this study, fresh leaves of E. wushanense were sampled from the Badong County of Hubei Province, China (N31°09′, E110°27′). Meanwhile, the voucher samples (0434) were collected and deposited at the Herbarium of the Institute of Medicinal Plant (IMPLAD), Beijing, China. Genomic DNA was extracted from the leaves using the improved CTAB method (Doyle 1987). Total DNA was used for the shotgun library construction. The library was sequenced on an Illumina Novaseq PE150 platform and 150 bp paired-end reads were generated. The clean reads were assembled using the program GetOrganelle v1.6.2 (Jin et al. 2018) with the reference chloroplast genome of E. acuminatum (GenBank accession number: NC_029941). The gene models were annotated using the online program CPGAVAS2 (Shi et al. 2019) and GeSeq (Tillich et al. 2017), followed by manual correction. The new annotated cp genome of E. wushanense had been submitted to NCBI database (accession number: MN857417).

The complete cp genome of E. wushanense is 157,283 bp in length and has a typical quadripartite structure, consisting of a large single-copy (LSC) region of 88,579 bp, a small single-copy (SSC) region of 17,082 bp, and two inverted repeat regions (IRa and IRb) of 25,811 bp. The GC content of complete chloroplast genome, LSC, SSC, and IR regions is 38.78, 37.38, 32.75, 43.19%, respectively. The complete cp genome contains 112 unique genes, of which are 78 protein-coding genes, 30 tRNA, 4 rRNA genes. The genes duplicate in the IR region, which are five protein-coding genes (ndhB, rpI23, rps7, ycf2, and rps12), seven tRNA genes (trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, trnV-GAC, and trnA-UGC) and four rRNA genes (rrn16, rrn23, rrn4.5, and rrn5). Among all genes, 15 genes contained one intron and three genes contained a pair of introns.

To investigate the phylogenetic relationship of E. wushanense, a total of 19 complete cp genome sequences from related species in Berberidaceae was downloaded from the NCBI database. After aligning using MEGA7 (Kumar et al. 2016), RAxML GUI1.5b2 (Stamatakis 2014) was used to reconstruct a Maximum-Likelihood (ML) phylogenetic tree, with Arabidopsis thaliana as the outgroup (Figure 1). As a result, phylogenetic analysis indicated that E. wushanense is closely related to E. pseudowushanense, E. lishihchenii, and E. sagittatum. The complete cp genome of E. wushanense would be a useful resource for studies on population genetics, molecular ecology, molecular identification, and evolution of Epimedium and related plant groups.

Figure 1.

Figure 1.

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Maximum-likelihood (ML) phylogenetic tree based on complete chloroplast genomes of 19 species, with Arabidopsis thaliana as the out group. Numbers above the lines represent ML bootstrap values.

Funding Statement

This work was supported by the CAMS Innovation Fund for Medical Sciences (CIFMS) [2017-12 M-3-013], the National Natural Science Foundation of China [81473302], the Chongqing Science and Technology Bureau [cstc2018jcyjAX0316, cc-cstc-CA-19-2], and the Traditional Chinese Medicine Science and the Technology Projects of Chongqing Health and Family Planning Commission [ZY201802117].

Disclosure statement

No potential conflict of interest was reported by the authors.

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