The complete chloroplast genome of Epimedium pubescens Maxim. (Berberidaceae), a traditional Chinese medicine herb

Abstract

Epimedium pubescens Maxim. is a well-known traditional Chinese medicine herb. In this study, the complete chloroplast genome of E. pubescens was sequenced. The genome was 158 956 bp in length, with a large single-copy region of 86,345 bp, a small single-copy region of 17,075 bp, and 2 inverted repeat regions of 27,768 bp. The genome consisted of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC contents were 38.82%. Phylogenetic analysis showed that E. pubescens of series Brachyrcerae was firstly clustered with E. acumiantum Franch. of ser. Dolichocerae, but not with E. brevicornu Maxim. from the same series.

Keywords:

• Epimedium pubescens
• chloroplast
• genome sequence
• medicinal plant

Epimedium L. contains about 62 species and is the largest herbaceous genus of Berberidaceae (Ying et al. 2011; Y. Zhang et al. 2016; Y.J. Zhang et al. 2020). The overwhelming majority of Epimedium species are endemic to China, although some are found in eastern, southern, and central Asia as well as in Europe (Ma et al. 2011). More than 15 Epimedium species have been used as Chinese medicine and shown curative effects for sexual dysfunction, osteoporosis, cardiovascular diseases, asthma, menstrual irregularity, chronic nephritis, cancer, and so on (Jiang et al. 2015; Indran et al. 2016; Tan et al. 2016). However, Epimedium is a complex taxon and still has many questions on its infra-genetic phylogeny and species identification. Chloroplast genome has been widely utilized for reconstructing phylogenetic relationships and development of DNA barcodes and molecular markers for the identification of plant species/strains (Jansen et al. 2007; Avise 2009; Jung et al. 2014). In the previous studies, 16 Epimedium species have been reported (Lee et al. 2016; Zhanget al. 2016; Sun et al. 2018; Guo et al. 2019; Zhang et al. 2020). In the present paper, the complete chloroplast genome of Epimedium pubescens Maxim., one of the four original plants of Herba Epimedii in Chinese Pharmacopeia (The state Pharmacopoeia Committee of China 2015), was sequenced and the phylogenetic relationship of Epimedium was analyzed.

The chloroplast DNA of Epimedium pubescens was extracted from its fresh leaves materials which were collected in Dujiangyan, Sichuan, China (N31°0′11.65″; E103°36′32.51″). Voucher Yanjun Zhang 555 (HIB) was deposited in the Herbaria of Wuhan Botanical Garden, Chinese Academy of Sciences (HIB). A chloroplast genomic library was constructed with PCR technology and sequenced with Illumina Hiseq 2000 (Kim et al. 2017). High-quality reads were obtained with raw reads and assembled using NGS QC (Cai et al. 2015). Genome was assembled using CLC Genomics Workbench 11.0 software (CLC Bio, Aarhus, Denmark) and annotated using DOGMA (http://phylocluster.biosci.utexas.edu/dogma/) combined with the online alignment tools Blastx and ORF Finder (http://www.ncbi.nlm.nih.gov/).

The chloroplast genome sequence of Epimedium pubescens was submitted to NCBI, and the accession number was MN747095. The genome sequence was158,956 bp in length and the structure was a typical quadripartite, consisting of a large single-copy region with 86,345 bp (LSC), a small single-copy region with 17,075 bp (SSC), and two inverted repeat regions with 27,768 bp (IRs). The GC contents in the chloroplast genome were 38.82%. The chloroplast genome of E. pubescens contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes.

The maximum likelihood tree was constructed based on the genome sequences of Epimedium pubescens, 16 reported Epimedium species and Vancouveria hexandra as outgroup (Hansen et al. 2007) using MEGA7.0 (Kumar et al. 2016) (Figure 1). The results were basically in accord with the previous phylogenetic trees based on chloroplast genome sequences of Epimedium (Y. Zhang et al. 2014, 2016; Y.J. Zhang et al. 2020). Epimedium pubescens of series Brachyrcerae was firstly clustered with E. acumiantum Franch. of ser. Dolichocerae, but not with E. brevicornu Maxim. from the same series. The phylogeny of Epimedium needs further study based on more chloroplast genome data of the genus.

Figure 1. A phylogenetic ML tree constructed using MEGA7.0 based on the complete chloroplast sequence of 17 Epimedium species including E. pubescens and that of Vancouveria hexandra as outgroup.

Disclosure statement

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

Data availability

The data that support the findings of this study will be available in GenBank at https://www.ncbi.nlm.nih.gov/, Accession number MN747095.

Additional information

Funding

This research was supported by the National Natural Science Foundation of China [31670346], the National Science and Technology Infrastructure program of China-compilation of Ex Situ Cultivated Flora of Botanical Garden [2015FY210100], the Key Scientific Research Talents Project of Wuhan Botanical Garden, Chinese Academy of Sciences [Y855281A05] and the Application Foundation Frontier Project of Wuhan Science and Technology Bureau [2019020701011435].