Characterization of the complete chloroplast genome of American ginseng, Panax quinquefolius L.

Abstract

American ginseng, Panax quinquefolius L. is one of the most widely used and perennial understory herbal remedies in the world, belongs to the Araliaceae family. It is native to Canada, Eastern United States, and North America. American ginseng has always been known as ‘green gold’ in North America. In this study, the complete chloroplast genome of P. quinquefolius L. was determined by the BGISEQ-500 Sequencing. The complete chloroplast genome of American ginseng, (P. quinquefolius L.) was 156,267 bp in length and displays a typical quadripartite structure of the large (LSC, 86,124 bp) and small (SSC, 18,069 bp) single-copy regions, separated by a pair of inverted repeat regions (IRs, 26,037 bp each). It harbours 133 functional genes, including 89 protein-coding genes, 36 transfer RNA, and 8 ribosomal RNA genes species. The overall nucleotide composition was: 30.6% A, 31.4% T, 19.4% C, and 18.6% G, with a total G + C content of 38.0%. Phylogenetic relationship analysis shows that P. quinquefolius L. closely related to Panax ginseng.

Keywords:

• American ginseng
• Panax quinquefolius L
• chloroplast genome
• HomBlocks
• phylogenetic relationship

American ginseng, Panax quinquefolius L. has been recommended for years as a traditional medicine in America, Canada, North America, China, and East Asia (Cruse-Sanders and Hamrick 2004). The major bioactive components of American ginseng are the triterpene saponins known as ginsenosides. American ginseng contains Rb1, Rd, and Re ginsenoside higher than Panax ginseng and Ro ginsenoside is only found saponin in American ginseng (Asafu-Adjaye and Wong 2003). It also has been used as a medicinal herb for a multitude of diseases such as cancer, diabetes, cardiovascular ills, and obesity (Wu et al. 2013). In this study, the complete chloroplast of American ginseng, P. quinquefolius L. was determined and the phylogenetic relationship analysis was carried out, which contributes to the further research and contribute to the conservation of medicinal plants valuable genetic resource

The specimen of P. quinquefolius L. was isolated from Jilin Agricultural University D06 test field in Changchun, Jilin, China (125.40E; 43.82N) and the DNA of P. quinquefolius L. was stored in Jilin Agricultural University College of Life Science (No. JLAUCLS8). The American ginseng DNA sample was sequenced using the BGISEQ-500 Sequencing (BIG, Shenzhen, CA, CHN). The American ginseng complete chloroplast genome was preliminarily annotated using by BLAST and DOGMA online program (Wyman et al. 2004), with default settings to identify protein-coding genes, rRNAs, and transfer RNAs (tRNAs) based on the Plant Plastid Code and BLAST homology searches. The secondary structures of tRNA genes were identified by using the ARAGORN (Laslett and Canback 2004) or through manually visual inspection.

The chloroplast genome sequence of P. quinquefolius L. is a closed-circular molecule of 156,267 bp in length, containing a large single copy region (LSC) of 86,124 bp, a small single copy region (SSC) of 18,069 bp, and a pair of inverted repeat regions (IRs) of 26,037 bp. In total 133 genes were annotated on this chloroplast genome, including 89 protein-coding genes (PCG), 36 tRNA genes, and 8 ribosomal RNA genes (rRNA). In the IR regions, a total of 16 genes were found duplicated, including 5 PCG species (rps19, rpl2, rpl23, rps7, and rps12), 7 tRNA species (trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, and trnN-GUU), and 4 rRNA species (rrn16, rrn23, rrn4.5, and rrn5). The overall nucleotide composition is: 30.6% A, 31.4% T, 19.4% C, and 18.6% G, with a total G + C content of 38.0%.The annotated chloroplast genome was submitted to GenBank database under accession No.MH056423.

For the phylogenetic relationship, we selected P. quinquefolius L. and other 34 plants chloroplast genomes from GenBank to assess between them. The genome-wide alignment of all plant complete chloroplast genomes was done by HomBlocks (Bi et al. 2018). The phylogenetic trees were reconstructed using Maximum-likelihood (ML) methods. ML phylogenetic tree was constructed using MEGA-X with 5000 bootstrap replicate (Kumar et al. 2018). All the nodes were inferred with strong support by the ML methods. As shown in the phylogenetic tree (Figure 1), the chloroplast genome of P. quinquefolius L. showed the closest with P. ginseng.

Figure 1. Phylogenetic tree of Panax quinquefolius L. and other 34 plant complete chloroplast genomes which yielded by Maximum-likelihood analysis. The phylogenetic tree was drawn without setting outgroup. All nodes exhibit above 90% bootstraps. The length of branch represents the divergence distance. The NCBI database accession number of Panax quinquefolius L. to Panax ginseng in the counterclockwise direction is KP036468.1, KX247147.1, KU059178.1, KT748629.1, KC456166.1, KC456167.1, KX510276.1, MG255756.1, MF579702.1, KT274029.1, MG255767.1, MG255759.1, MG255752.1, LN515489.1, MG255753.1, MG255758.1, KY646163.1, KR232566.1, HF586694.1, KY751712.1, KU724141.1, KY562590.1, MG770330.1, KU170194.1, KT959111.1, KF150644.2, MF861203.1, KP718626.1, KP718628.1, MF861202.1, KT724052.1, KT633216.1, KY085895.1, KM067389.1.

Disclosure statement

The authors have declared that no competing interests exist.

Additional information

Funding

This work was supported by the Doctoral Scientific Research Foundation of Jilin Agricultural University [201618].