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.

Keywords:

• Berberidaceae
• chloroplast genome
• Epimedium shuichengense

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′26.74″, E 104°44′33.13″), 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).

The complete cp genome of E. shuichengense (GenBank accession number: MN939631) is 157,056 bp in length, displaying a quadripartite structure that contains a pair of inverted repeats (IR) regions (20,820 bp), separated by a large single-copy (LSC) region (88,346 bp) and a small single-copy (SSC) region (26,768 bp). There are 130 genes reported, including 8 rRNA genes, 37 tRNA genes, and 85 protein-coding genes. The overall GC content of the chloroplast genome was 38.8%, the GC content in LSC, SSC, and IR regions was 37.4%, 32.8%, and 43.2%, respectively. A total of 20 genes (trnK-UUU, trnI-GAU × 2, trnA-UGC × 2, trnG-UCC, trnV-UAC, trnL-UAA, rpoC1, ndhB × 2, ndhA, rpl16, rpl2, petB, atpF, petD, rps16, rps12 × 2) contained 1 intron, and 2 genes (clpP, ycf3) contained 2 introns.

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.

Figure 1. Phylogenetic tree produced by maximum likelihood (ML) analysis base on chloroplast genome sequences from 18 species of Epimedium, Nandina and Berberis. Shown next to the nodes are bootstrap support values based on 1000 replicates.

Disclosure statement

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

Additional information

Funding

This work was supported by China Guizhou Provincial Science & Technology Department [Grant No. [2019]5658]; China Guizhou Provincial Education Department [Grant No. KY[2017]018]; Special subsidy for public health services of traditional Chinese medicine [Grant No. 2018-132], and Ministry of Science and Technology [2018YFC1708101].