Characterization of the complete chloroplast genome of Artemisia capillaris (Campanulales: Asteraceae Bercht), a unique economic plant to China

Abstract

Artemisia capillaris is an endemic annual herb of Artemisia (Asteraceae Bercht) in China. The seedlings in early spring, removed old stems and impurities to dry, as a commonly used traditional Chinese medicine, has been listed in the Chinese Pharmacopoeia. The A. capillaris methanol (MeOH) extracts showed antioxidative activity and anticancer activity.

The complete chloroplast (cp) genome was assembled by Illumina paired-end reads data. The circular cp genome is 151,074 bp in size, including a large single copy (LSC) region of 82,837 bp, a small single copy (SSC) region of 18,309 bp, and a pair of inverted repeat (IRs) regions of 24,964 bp. Besides, 11 genes possess a single intron, while another three genes ycf3, rps12, and clp have a couple of introns. The GC content of the entire A. capillaris cp genome, LSC, SSC, and IR regions are 37.58, 30.7, 32.3, and 43.1%, respectively. Based on the concatenated coding sequences of cp PCGs, the phylogenetic analysis showed that A. capillaris and A. selengensis are closely related to each other within the family Compositae.

Keywords:

• Artemisia capillaris
• Compositae
• chloroplast genome
• Illumina sequencing
• phylogenetic analysis

Artemisia capillaris is a traditional medicinal plant in China (Wang et al. 2013), which contains a variety of chemicals, including Dimethylesculetin (DME), Capillarisin, Chlorogenic acid (Chen et al. 1987). Previous studies have shown that DME has a significant hepatoprotective effect (Zhang et al. 2011), Capillarisin showed antioxidative activity and could enhance liver detoxification (Dou et al. 2007, 2013), Chlorogenic acid showed anticancer activity (Hou et al. 2013). In Asia, A. capillaris was widely used to prevent and treat jaundice and work on stomach and spleen (Chevallier 1996; Huang et al. 2004).

The conserved quadripartite structure of a typical circular cp genome includes a pair of inverted repeats (IRs), separated by a large single-copy region (LSC), and a small single-copy region (SSC) (Wolfe et al. 1992; Lee et al. 2007). This study will be very useful for the research on the phylogenetic relationships of A. capillaris and Compositae.

Fresh leaves of A. capillaris were collected from the Botanical Garden of Northwest University (34°16′N, 108°54′E; Shaanxi, NW China). A voucher specimen (AC181212) is deposited at the Pharmacognosy laboratory, the Department of Pharmacy in Xi’an International University. We used the modified CTAB method to extract the total genomic DNA (Doyle and Doyle 1987). A shotgun library constructed following the manufacturer’s protocol for the Illumina HiSeq X Ten Sequencing System (Illumina, San Diego, CA, USA). We assembled the cp genome using the program MITObim v1.8 (https://github.com/chrishah/MITObim) (Hahn et al. 2013), with that of Artemisia selengensis (GenBank:MH042532) as the initial reference. The web-based tool OGDRaw v1.2 (http://ogdraw.mpimp-golm.mpg.de/) was employed to generate a map of the complete cp genome (Lohse et al. 2013). The complete cp genome sequence has been submitted to GenBank (accession number MK590021).

The complete cp genome is a circular and double-stranded DNA molecule with a typical quadripartite structure, containing two inverted repeat (IRs) regions, a large single copy (LSC) region and a small single copy (SSC) region. In all, we received 23,707,228 raw paired-end reads, of which the length distribution is 151,074 bp (GC, 37.5%), the length of LSC region, IRs regions, and SSC region is 82,837 (GC, 35.6%), 24,964 (43.1%), and 18,309 (30.7%) respectivly.

It encodes 133 complete genes, including 88 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In addition, 9 PCG genes (atpF, ndhA, ndhB, rps16, rpl2, rpl16, rpoC1, petD, and petB) possess a single intron, 71 PCG genes no intron, 3 other genes (clpP, rps12, and ycf3) harbor two introns, 6 tRNA genes (trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) harbor a single intron.

To investigate the phylogenetic position of A. capillaris, we constructed a neighbour-joining (NJ) phylogenetic tree (Figure 1) based on the concatenated coding sequences of 17 chloroplast PCGs for 17 plastid genomes from published species of Compositae using MEGA7 with 1000 bootstrap replicates (Kumar et al. 2016) (http://www.megasoftware.net/). From the phylogenetic tree analysis, we find that A. capillaris and Artemisia selengensis (MK590021) are closely related to each other within the family Compositae (Figure 1).

Figure 1. Maximum likelihood (ML) tree of Artemisia capillaries and its related relatives based on the complete chloroplast genome sequences.

Disclosure statement

The authors report no conflicts of interest, and are solely responsible for the content and writing of this paper.

Additional information

Funding

This work was supported by a grant from the Natural Science Foundation of Education department of Shaanxi province, China [No.15JK2118].