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Authentication markers for five major Panax species developed via comparative analysis of complete chloroplast genome sequences Van Binh Nguyen, Hyun-Seung Park, Sang-Choon Lee, Junki Lee, Jee Young Park, and Tae-Jin Yang J. Agric. Food Chem., Just Accepted Manuscript • Publication Date (Web): 22 May 2017 Downloaded from http://pubs.acs.org on May 23, 2017

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Journal of Agricultural and Food Chemistry

Authentication markers for five major Panax species developed via comparative analysis of complete chloroplast genome sequences

Van Binh Nguyena, Hyun-Seung Parka, Sang-Choon Leea, Junki Leea, Jee Young Parka, TaeJin Yanga,b* a

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute

of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. b

Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University,

Pyeongchang 232-916, Republic of Korea. *Corresponding author: Tae-Jin Yang E-mail: [email protected] Tel: +82-2-880-4547, Fax: +82-2-877-4550

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Abstract

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Ginseng represents a set of high-value medicinal plants of different species: Panax

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ginseng (Asian ginseng), P. quinquefolius (American ginseng), P. notoginseng (Chinese

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ginseng), P. japonicus (Bamboo ginseng), and P. vietnamensis (Vietnamese ginseng). Each

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species is pharmacologically and economically important, with differences in efficacy and

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price. Accordingly, an authentication system is needed to combat economically motivated

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adulteration of Panax products. We conducted comparative analysis of the chloroplast

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genome sequences of these five species, identifying 34–124 InDels and 141–560 SNPs.

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Fourteen InDel markers were developed to authenticate the Panax species. Among these,

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eight were species-unique markers that successfully differentiated one species from the others.

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We generated at least one species-unique marker for each of the five species, and any of the

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species can be authenticated by selection among these markers. The markers are reliable,

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easily detectable, and valuable for applications in the ginseng industry as well as in related

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research.

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Keywords: Panax species, Chloroplast genome, Molecular markers, Ginseng authentication

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Journal of Agricultural and Food Chemistry

Introduction

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The Panax genus belongs to the Araliaceae family and contains many important

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medicinal species, collectively called ‘ginseng’. Of the 14 known species in the Panax genus,

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five species, Panax ginseng (Asian ginseng), P. quinquefolius (American ginseng), P.

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notoginseng (Sanchi ginseng; Chinese ginseng), P. japonicus (Bamboo ginseng), and P.

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vietnamensis (Vietnamese ginseng), are broadly utilized in Korea, the USA, China, Japan,

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and Vietnam. Each species is well-known as a traditional medicinal plant in oriental countries,

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and species such as P. ginseng, P. quinquefolius, and P. notoginseng contain

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protopanaxadiol-type and protopanaxatriol-type saponins1, while other species like P.

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japonicus and P. vietnamensis contain high quantities of oleanolic acid-type and ocotillol-

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type saponins, respectively1,2.

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The high pharmacological and economical value of ginseng means that many

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economically motivated adulterations (EMAs) of ginseng products have been developed by

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substituting morphologically similar plant roots, or by mixing different species. Traditionally,

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the authentication of herb plants was based on morphological and histological inspection.

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However, these traditional methods are unable to authenticate some Panax species because of

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their very similar morphological appearances, especially in terms of root shape. For example,

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P. ginseng and P. quinquefolius, and P. japonicus and P. vietnamensis cannot easily be

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distinguished from each other. Moreover, many commercial ginseng products are sold in a

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processed form, such as red ginseng, ginseng powder, liquid extracts, pellets, shredded slices,

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or even tea, which cannot be authenticated by traditional methods. Ginsenoside profiling

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methods have been developed to authenticate ginseng samples3. However, the effects of

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factors such as growth conditions, developmental stage, internal metabolism, storage

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conditions, and manufacturing processes on secondary metabolite accumulation in ginseng

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limits the application of such chemical analyses4. Chemical methods are also expensive and

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difficult to utilize in high-throughput analysis. Therefore, reliable and practical methods to

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authenticate ginseng are in high demand.

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The chloroplast is a plant-specific organelle containing the entire machinery required for

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photosynthesis and carbon fixation. Chloroplast genomes are generally highly conserved

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across land plants at the gene level, with a quadripartite structure comprising two inverted

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repeat blocks (IRs), one large single copy (LSC) region, and one small single copy (SSC)

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region. As a result of interspecies sequence divergence and intraspecies sequence

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conservation, the chloroplast genome is valuable for taxonomic classification and phylogeny

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reconstruction5,6. Lack of recombination, low nucleotide substitution rates, and usually

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uniparental inheritance make chloroplast genomes valuable sources of genetic markers for

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phylogenetic analysis and species identification7,8. Chloroplast sequences such as atpF-atpH,

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matK, psbK-psbI, rbcL, ropC1, rpoB, and trnH-psbA are commonly used as DNA barcodes

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for plants9-11. In some cases, these sequences were highly efficient for species identification

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and phylogenetic studies, but they showed low variation in closely related species10.

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Recently, DNA markers have been developed to authenticate ginseng, including random

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amplified polymorphic DNA (RAPD)12, microsatellite13, and expressed sequence tag-simple

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sequence repeat (EST-SSR)14,15 markers, as well as single nucleotide polymorphism (SNP)

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and insertion and deletion (InDel) markers derived from chloroplast sequences6,16,17.

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However, thus far, these markers have been used to identify only P. ginseng cultivars at the

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intraspecies level, and just a few Panax species at the interspecies level.

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Recently, we developed an efficient method to obtain complete chloroplast genome and

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nuclear ribosomal DNA (nrDNA) by de novo assembly using low-coverage whole-genome

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shotgun next-generation sequencing (dnaLCW)18. Using this method, we obtained complete

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chloroplast genomes and nrDNA for the five Panax species: P. ginseng, P. quinquefolius, P.

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notoginseng, P. japonicus, and P. vietnamensis6,19. In the present study, we comparatively

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analyzed these five chloroplast genome sequences and developed credible chloroplast

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genome-derived InDel markers to authenticate these Panax species. These markers are

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valuable tools for the further study of genetic diversity in the Panax genus. They also may be

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used to support the ginseng industry, which depends on a number of Panax species, for

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example, P. ginseng in Korea, China, and Japan, P. quinquefolius in the USA, Canada, and

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China, P. notoginseng in China, and P. vietnamensis in Vietnam.

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Materials and Methods

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Plant materials and Genomic DNA extraction

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P. ginseng (cultivars ‘Chunpoong’ (CP) and ‘Yunpoong’ (YP)) and P. quinquefolius

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plants were collected from the ginseng farm at Seoul National University in Suwon, Korea. P.

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notoginseng and P. japonicus plants were collected from Dafang County, Guizhou Province,

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and Enshi County, Hubei Province, China, respectively. P. vietnamensis plants were collected

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from Ngoc Linh Mountain, Kon Tum Province, Vietnam. Individual leaves and roots of

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plants from each species were harvested and stored at −70°C until use. Total genomic DNA

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was isolated using a modified cetyltrimethylammonium bromide (CTAB) method20. The

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quality and quantity of extracted genomic DNA was measured using a UV-spectrophotometer.

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Comparative analysis and characterization of SSRs and large sequence repeats

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The chloroplast genome sequences of P. ginseng cv. CP (KM088019), P. ginseng cv. YP

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(KM088020), P. quinquefolius (KM088018), P. notoginseng (KP036468), P. japonicus

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(KP036469), and P. vietnamensis (KP036471) were obtained from our previous studies6,19.

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MAFFT

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(http://genome.lbl.gov/vista/mvista/submit.shtml) programs were used to compare these

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sequences.

(http://mafft.cbrc.jp/alignment/server/),

MEGA

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and

mVISTA

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SSRs were predicted using MISA (http://pgrc.ipk-gatersleben.de/misa/misa.html)22 with

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the parameters set to ≥10 repeat units for mononucleotide SSRs, ≥5 repeat units for

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dinucleotide SSRs, ≥4 repeat units for trinucleotide SSRs, and ≥3 repeat units for

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tetranucleotide, pentanucleotide, and hexanucleotide SSRs.

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The program REPuter23 was used to identify the number and location of repeat sequences,

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including tandem, dispersed, reverse, and palindromic repeats within chloroplast genomes.

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For all repeat types, the following constraints were set to a minimum repeat size of 15 bp, and

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90% minimum cut-off identity between two copies. Overlapping repeats were merged into

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one repeat motif whenever possible.

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Development and validation of InDel markers

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To validate intraspecies and interspecies polymorphism in the chloroplast genomes, and

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develop DNA markers to authenticate the five major Panax species, specific primers were

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designed based on InDel polymorphic sites found in Panax chloroplast genomes, including P.

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ginseng cv. YP (KM088020) as an intraspecies level. Primer pairs were designed using the

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Primer3 program (http://bioinfo.ut.ee/primer3-0.4.0/).

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The polymerase chain reaction (PCR) was performed in a 25 µl reaction mixture

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containing 20 ng of DNA template, 5 pmol of each primer, 1.25 mM deoxynucleotide

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triphosphate (dNTP), 1.25 units of Taq DNA polymerase (Inclone, Korea), and 2.5 µl of 10×

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reaction buffer. The PCR reaction was performed in thermocyclers using the following

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cycling parameters: 94°C (5 min); 35 cycles of 94°C (30 s), 54–58°C (30 s); 72°C (30 s),

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then 72°C (7 min). PCR products were visualized on agarose gels (1.5–3.0%) after staining

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with ethidium bromide, and/or analyzed by capillary electrophoresis using a fragment

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analyzer (Advanced Analytical Technologies Inc., USA).

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Results

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Journal of Agricultural and Food Chemistry

Structure of complete chloroplast genomes of five Panax species

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Complete chloroplast genomes of five Panax species were obtained by dnaLCW and

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reported in our previous studies6,19. Lengths of the chloroplast genomes ranged from 155,993

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bp (P. vietnamensis) to 156,466 bp (P. notoginseng). The order, content, and orientation of

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genes were highly conserved among these five chloroplast genomes, comprising 79 protein-

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coding genes, 30 tRNA genes, and 4 rRNA genes in common. Each chloroplast genome had

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the same quadripartite structure with an LSC, an SSC, and two IR regions (Fig. 1).

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Variations in the copy numbers of SSRs were identified among the five Panax chloroplast

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genomes. The longest SSRs were 18 nucleotides in length, and the most abundant nucleotides

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in SSRs were A and T (Table 1). P. vietnamenis and P. notoginseng both contained 42 SSRs;

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lower than P. japonicus (45), and higher than P. ginseng cv. CP (38) and P. quinquefolius (40)

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(Table 1). The P. japonicus chloroplast genome has the highest number of homopolymers

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(24), but no hexapolymers. P. vietnamensis, P. notoginseng, and P. ginseng cv. CP all had 6

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dipolymers; lower than P. japonicus and P. quinquefolius (7). P. notoginseng had 4

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tripolymers; more than each of the other Panax species (3). P. vietnamensis had 10

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tetrapolymers; more than the other Panax species (8). P. japonicus and P. notoginseng had 3

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pentapolymers each, while the other Panax species contained 2 (Table 1).

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For comparative analysis, repetitive sequences were grouped into four categories: tandem,

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dispersed, palindromic, and reverse. To avoid redundancy, repeat sequence analysis of each

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chloroplast genome was carried out with a single IR region. A total of 45–50 repetitive

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sequences were identified in each of the five Panax chloroplast genomes (Fig. 2B), including

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dispersed repeats (44.26%), palindromic repeats (29.79%), tandem repeats (22.13%), and

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reverse repeats (3.83%). Most repeats were located in intergenic spaces (IGS) (53.83%) and

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coding sequence (CDS) regions (38.94%); a small number of repeats (7.23%) were found in

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intron regions (Fig. 2C). Across the five chloroplast genomes, repeat lengths ranged from

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17 bp to 67 bp (Fig. 2A). The 67-bp tandem repeat found in P. japonicus was the longest

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repeat (Fig. 2A). Palindromic and reverse repeats ranged from 17–35 bp and 17–28 bp,

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respectively (Fig. 2A). Comparing the length and location, 32 repeats were shared by all five

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Panax species, and 5 repeats were present in four chloroplast genomes. P. notoginseng had

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the most unique repeats (9), followed by P. ginseng and P. vietnamensis (6), P. japonicus (3),

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and P. quinquefolius (1) (Fig. 2D).

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Divergence of chloroplast genomes among Panax species

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To investigate chloroplast genome divergence among the five Panax species, multiple

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alignments of six chloroplast genomes were performed with a single IR region. The sequence

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identity of six chloroplast genomes was plotted using the mVISTA program, using the Panax

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ginseng cv. CP annotation as the reference (Fig. 3). Two cultivating varieties of ginseng, CP

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and YP, were almost identical with 3 InDels and 1 SNP overall (Table 2). Five Panax species

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also showed high sequence similarity with each other (98.9%) (Fig. 3), suggesting that Panax

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chloroplast genomes are well conserved. Our results are consistent with earlier research on

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Araliaceae chloroplast genomes8. As expected, coding regions are more conserved than non-

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coding regions. The most highly conserved chloroplast genome coding regions are the four

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rRNA and 30 tRNA genes (Fig. 3). The most divergent coding region is the ycf1 gene, which

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has low sequence identity because of various InDels and repeat sequences (Fig. 3). This has

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been reported in previous research on other chloroplast genomes8,24.

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Although chloroplast genome diversity at the intraspecies level is low, abundant

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polymorphism was identified between species. At the interspecies level, the number of SNPs

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ranged between 141 (P. ginseng versus P. quinquefolius) and 560 (P. ginseng versus P.

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vietnamensis), and the number of InDels ranged between 34 (P. ginseng versus P.

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quinquefolius) and 124 (P. notoginseng versus P. vietnamensis) (Table 2). A/T SNP

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substitutions were more frequent than other types, in agreement with previous studies5,25.

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Fewer substitutions and InDels were found between P. ginseng and P. quinquefolius than

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between the other three Panax species. The ratios of nucleotide substitution events to InDel

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events (S/I) for different pairwise comparisons between species ranged between 4.06 (P.

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ginseng versus P. quinquefolius) and 5.64 (P. quinquefolius versus P. japonicus) (Table 2).

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S/I ratios are thought to increase with divergence time between genomes26. Our results

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indicate that P. ginseng is more closely related to P. quinquefolius (S/I = 4.06), and that P.

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quinquefolius is more highly divergent from P. japonicus (S/I = 5.64), compared to others.

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Development of InDel markers to identify Panax species

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Based on chloroplast genome sequence alignment, the 14 most InDel-variable loci were

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selected to develop 14 potentially discriminate markers (Table 3; Fig. 1). Each of these 14

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markers were successfully amplified by PCR, and each showed the expected polymorphic

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band sizes. Eight of these 14 markers had unique amplicon sizes specific to different Panax

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species (Table 4).

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The marker gcpm2 was specific to both P. ginseng cultivars (CP and YP), and was

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derived from a 33-bp tandem repeat (TR) in the rps16–trnQ-UUG region (Table 4; Fig. 4B).

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The P. notoginseng-specific markers gcpm3, gcpm8, and gcpm10 were derived from a 25-bp

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TR in the atpH–atpI region, a 38-bp TR in the petA–psbJ region, and a 25-bp TR in the

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rpl14–rpl16 region, respectively (Table 4; Fig. 4C, H, K). The gcpm4 marker was derived

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from a 23-bp TR in the rps2–rpoC2 region, and was specific to P. quinquefolius (Table 4; Fig.

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4D). The marker gcpm6 was derived from a 67-bp TR and a 19-bp InDel in the trnE–trnT

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region, and was specific to P. japonicus (Table 4; Fig. 4F). Finally, the markers gcpm9 and

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gcpm14 were derived from a 25-bp TR and a 6-bp SSR in the clpP–psbB region, and a 30-bp

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InDel in ycf1, respectively, and were specific to P. vietnamensis (Table 4; Fig. 4I, O).

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Validation results revealed that six markers, gcpm1, 5, 7, 11, 12, and 13, were able to

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identify more than two species, of which gcpm12 (derived from a 57-bp TR in the ycf1 gene)

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was the most variable (Table 4; Fig. 4M). In addition, gcpm12 also distinguished between the

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two P. ginseng cultivars (Table 4; Fig. 4M).

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Discussion

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Repetitive sequences in Panax chloroplast genomes

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Repeat structure plays an important role in genomic rearrangement and divergence in

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chloroplast genomes via illegitimate recombination and slipped-strand mispairing27,28. SSRs

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are direct tandem repeated DNA sequences consisting of short (1–10 bp) nucleotide motifs.

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The highly polymorphic, non-recombinant and uniparentally inherited nature of SSRs means

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they are often used as genetic molecular markers for population genetics29,30, and the study of

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ecology and evolution. In this study, we found 207 SSRs (Table 1), varying in number and

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type between five major Panax species.

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It is considered that species divergence in chloroplast genomes is mostly caused by

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repetitive sequences. Indeed, we found many repetitive sequences associated with

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polymorphic chloroplast sites among the five major Panax species studied. Among the many

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repeats in the ycf3 gene, the most divergent target region was a 57-bp TR. TRs such as this

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can be used to develop molecular markers for the identification and authentication of Panax

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species6.

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Comparative analysis of Panax chloroplast genomes

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Polymorphism at the intraspecies level polymorphism is very low compared to that at the

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interspecies level. In P. ginseng, 12 chloroplast genomes derived from different cultivating

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varieties revealed over 99.9% sequence similarity, and only 6 InDels and 6 SNPs6.

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Meanwhile, of a total of 201 InDels and 962 SNPs identified among five Panax chloroplast

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genome sequences, 34–124 InDels and 141–560 SNPs were shared between two Panax

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species (Table 2). However, the chloroplast genome is highly conserved within Panax species,

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and has high similarity (≥98.9%) at the nucleotide sequence level.

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In chloroplast genomes, nucleotide substitution has been used to examine plant evolution

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and genome differentiation between species7,17. These InDel events are mainly attributed to

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the repetition of an adjacent sequence, probably resulting from slipped-strand mispairing in

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DNA replication31. InDels play a major role in genome size evolution and are increasingly

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used in phylogenetic studies32,33. S/I ratios have been reported to increase with divergence

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time between genomes26. In this study, we identified many SNPs and InDels from the

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complete chloroplast genomes of five major Panax species; S/I ratios ranged between 4.06 (P.

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ginseng versus P. quinquefolius) and 5.64 (P. quinquefolius versus P. japonicus) (Table 2).

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Along with their similar morphologies and distributions, this indicates that P. ginseng is

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closely related to P. quinquefolius (S/I = 4.06), and is consistent with previous reports34,35. P.

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quinquefolius is highly divergent from P. japonicus compared to others (S/I = 5.64).

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Use of molecular markers to authenticate ginseng species

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Biological diversity is a valuable and vulnerable natural resource. The first steps towards

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protecting and benefiting from national biodiversity are to sample, identify, and study

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biological specimens. The use of molecular markers (i.e., DNA barcoding) has a powerful

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role to play in attaining many of the Millennium Development Goals, and reaching the

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objectives of the Convention on Biological Diversity, by sustaining natural resources,

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protecting endangered species, and identifying pests and pathogens at any life stage so as to

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more easily control them. DNA barcoding can also help to monitor food, water and

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environment quality by studying contaminating organisms.

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Although relatively new, the use of molecular markers is well on its way to being

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accepted as a global standard for species identification, and will play a major role in the

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future of taxonomy36. DNA-based species identification offers enormous potential for the

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biological scientific community, educators, and the interested public. The complete

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chloroplast genome has a conserved sequence from 110–160 kbp, which far exceeds the

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length of commonly used molecular markers and provides greater variation to discriminate

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between closely related species37. The chloroplast genome is smaller in size and hundreds

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times of higher copy numbers in a cell compared with the nuclear genome and has solid

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interspecific divergence with lower intraspecific variation, which makes chloroplast genome-

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based marker is suitable as DNA barcoding target37.

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It is important to be able to authenticate natural health products (NHPs) from legal,

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economic, health and conservation viewpoints. NHPs are often trusted by the public to be

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safe; however, adulterated, counterfeit and low quality products can seriously threaten

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consumer safety38,39. Ginseng plants have high economic and medicinal value, thus there are

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many EMA ginseng products. The use of molecular methods to accurately identify the origins

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of ginseng products is important to the development of the ginseng industry in those countries

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where ginseng is cultivated, such as Korea, the USA, China, Japan, and Vietnam. Recently,

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the chloroplast genome sequences rbcL, matK, trnH-psbA, and trnL-trnF, and a nuclear

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internal transcribed spacer (ITS) of nuclear 45S ribosomal RNA genes, have successfully

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been used as molecular markers for several plant species9,40, but these loci have little

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variability in Panax36. Although many studies have sought to authenticate ginseng13-15,41,

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application remains limited because of a lack of genome information and comprehensive

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comparative genomic analysis against related Panax species.

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In this study, we developed chloroplast-derived, species-specific markers for each of five

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major Panax species. Among 14 molecular markers, three markers were specific to P.

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notoginseng, and two were specific to P. vietnamensis. P. ginseng, P. quinquefolius and P.

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japonicus could also each be identified by species-specific markers (Table 4; Fig. 4). We

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discovered different 57-bp tandem repeats in the ycf1 gene of different Panax chloroplast

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genomes, and this polymorphism proved powerful in the identification of Panax species

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(Table 4; Fig. 4M). However, the gcpm12 marker, derived from the ycf1 gene, unexpectedly

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produced two amplified bands from P. notoginseng, of which the A allele was the expected

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allele of the P. ginseng type; allele D was not expected, but was same as the allele of P.

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Vietnamese, although all other species gave rise to a single band (Table 4; Fig. 4A, M). We

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assume that these unexpected bands are derived from heteroplasmy of the target sequences

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caused by different IRA and IRB regions related to ycf1 gene sequences; alternatively, they

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could be caused by chloroplast DNAs transferred into the nuclear or mitochondrial

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genomes42-45. In our previous study6, we also found intra-species polymorphism in P. ginseng

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at this position, indicating that, although highly informative, the marker designed from this

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region may be confusing for species authentication. Overall, we suggest that intra-species

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polymorphism and a combination of several markers should be considered for credible

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authentication between different species.

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Abbreviation Used

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InDel, insertion or deletion; SNP, single nucleotide polymorphism; DNA, deoxyribonucleic

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acid; bp, base pair.

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Funding

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This work was supported by: the Cooperative Research Program for Agriculture Science &

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Technology Development of the Rural Development Administration (grant number

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PJ01100801); the Ministry of Food and Drug Safety (grant number 16172MFDS229,

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awarded in 2016); and the Bio & Medical Technology Development Program of the NRF,

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MSIP (grant number NRF-2015M3A9A5030733), Republic of Korea.

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34. Nguyen, B.; Kim, K.; Kim, Y. C.; Lee, S. C.; Shin, J. E.; Lee, J.; Kim, N. H.; Jang, W.;

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Choi, H. I.; Yang, T. J. The complete chloroplast genome sequence of Panax

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36. Zuo, Y.; Chen, Z.; Kondo, K.; Funamoto, T.; Wen, J.; Zhou, S. DNA barcoding of Panax species. Planta Med. 2011, 77, 182. 37. Li, X.; Yang, Y.; Henry, R. J.; Rossetto, M.; Wang, Y.; Chen, S. Plant DNA barcoding: from gene to genome. Biol Rev. 2015, 90, 157-166. 38. Mine, Y.; Young, D. Regulation of natural health products in Canada. Food Sci Technol Res. 2009, 15, 459-468.

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39. Wallace, L. J.; Boilard, S. M.; Eagle, S. H.; Spall, J. L.; Shokralla, S.; Hajibabaei, M.

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mostly occur by replication slippage and show a biased pattern in the plastome of

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Oenothera. The Plant Cell. 2016, 28, 911-29.

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43. Park, S.; Ruhlman, T. A.; Sabir, J. S.; Mutwakil, M. H.; Baeshen, M. N.; Sabir, M. J.;

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Baeshen, N. A.; Jansen, R. K. Complete sequences of organelle genomes from the

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medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial

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genome evolution across asterids. BMC genomics. 2014, 15, 405.

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44. Goremykin, V. V.; Salamini, F.; Velasco, R.; Viola, R. Mitochondrial DNA of Vitis

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110.

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45. Matsuo, M.; Ito, Y.; Yamauchi, R.; Obokata, J., The rice nuclear genome continuously

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DNA flux. The Plant Cell. 2005, 17, 665-675.

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420

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FIGURE CAPTIONS

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Fig. 1. Complete chloroplast genomes of five Panax species.

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Colored boxes show conserved chloroplast genes, classified based on product function.

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Genes shown inside the circle are transcribed clockwise, and those outside the circle are

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transcribed counterclockwise. Genes belonging to different functional groups are color-coded.

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Dashed area in the inner circle indicates the GC content of the chloroplast genome; blue

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triangles indicate the positions of 14 markers (gcpm1–gcpm14) on the chloroplast genomes.

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Fig. 2. Repeat structure analysis of the five Panax species chloroplast genomes.

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(A) Histogram showing the frequency of repeats by length in the five Panax chloroplast

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genomes.

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(B) Histogram showing the number of four repeat types in each Panax chloroplast genome.

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(C) Location of the 235 repeats on the five Panax species chloroplast genomes.

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(D) Venn diagram showing the repeats shared among the five Panax species.

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Fig. 3. Comparison of chloroplast genome sequences of five Panax species.

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Pair-wise comparison of chloroplast genomes between Panax species using the mVISTA

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program with P. ginseng cv. CP as the reference. Genome regions are color-coded as protein

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coding (purple), rRNA or tRNA coding genes (blue), and noncoding sequences (pink).

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Fig. 4. Validation of 14 molecular markers derived from InDel regions of five Panax

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chloroplast genomes.

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Schematic diagrams indicate InDel regions between Panax species. Tandem repeats and

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inserted sequences are designated by pentagons and diamonds, respectively. Dotted and solid

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lines indicate deleted and conserved sequences; left and right black arrows indicate forward

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and reverse primers, respectively. The 14 InDel markers are denoted gcpm1 to gcpm14.

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Different alleles are shown via capillary electrophoresis (A – F, I, N), and agarose gel

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electrophoresis (G, H, K – M, O). Abbreviated species names shown on schematic diagrams 20 ACS Paragon Plus Environment

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and amplicons: PgCP, P. ginseng cv. CP; PgYP, P. ginseng cv. YP; Pq, P. quinquefolius; Pn,

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P. notoginseng; Pj, P. japonicus; Pv, P. vietnamensis; M, 100-bp DNA ladder.

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Table 1. SSRs in the five Panax chloroplast genomes. Number of SSRs Motif

Repeat units

PgCP

Pq

Pn

Pj

Pv

A/T

14

16

19

17

17

C/G

4

3

1

7

3

AT/AT

6

7

6

7

6

AAG/CTT

1

1

1

1

1

AAT/ATT

1

1

3

2

2

AGC/CTG

1

1

-

-

-

AAAG/CTTT

3

3

3

3

3

AAAT/ATTT

2

2

2

2

4

AATT/AATT

1

1

1

1

1

ACCT/AGGT

2

2

2

2

2

AATCT/AGATT

2

2

2

2

2

AAAAT/ATTTT

-

-

1

1

-

AGATAT/ATATCT

-

-

-

-

1

ACTATG/AGTCAT

1

1

1

-

-

38

40

42

45

42

Mononucleotide Dinucleotide

Trinucleotide

Tetranucleotide

Pentanucleotide

Hexanucleotide Total SSRs

Abbreviations: PgCP, P. ginseng cv. CP; Pq, P. quinquefolius; Pn, P. notoginseng; Pj, P. japonicus; Pv, P. vietnamensis; SSR, simple sequence repeat.

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Table 2. Numbers and ratios of nucleotide substitutions and InDels among chloroplast genomes of five Panax species. PgCP

PgYP

Pq

Pn

Pj

Pv

PgCP

/

1

141

480

511

559

PgYP

3 (0.33)

/

142

481

512

560

Pq

34 (4.15)

35 (4.06)

/

509

508

542

Pn

101 (4.75)

98 (4.91)

110 (4.63)

/

484

548

Pj

92 (5.55)

93 (5.51)

90 (5.64)

111 (4.36)

/

331

102 (5.48) 103 (5.44) 104 (5.21) 124 (4.42) 74 (4.47) / Pv Note: The upper triangle shows the total nucleotide substitutions, while the lower triangle indicates the number of InDels. Ratios of nucleotide substitutions to InDels (S/I) are given in brackets. Abbreviations: PgCP, Panax ginseng cv. CP; PgYP, P. ginseng cv. YP; Pq, P. quinquefolius; Pn, P. notoginseng; Pj, P. japonicas; Pv, P. vietnamensis.

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Table 3. Molecular markers developed to authenticate Panax species. Melting Expected PCR product size (bp) temperature PgCP PgYP Pq Pn Pj Pv (°C) a F: TGGGGGAATAAATAAGGAAGAA 54.7 gcpm1 392 392 393 391 416 430 R: TTAAAGAAGGCGGAGGTTTTTa 54.0 b F: TGGAAAGGCTGTTGTCACTG 53.2 gcpm2 194 194 161 160 161 161 R: TGCCAAGATTGCAGAAAGATTb 53.8 F: TGGTCAATCGCTGAAGAAAAa 53.2 gcpm3 449 449 449 474 449 449 R: CCGCGGCTTATATAGGTGAAa 57.3 F: CTCTTCCAAATTGATGTTCCAAa 56.6 gcpm4 295 295 318 295 295 295 R: TCCATGATACACCAGAACAATCAa 59.3 F: TCCTGAACCACTAGACGATGGa 53.3 gcpm5 457 457 457 465 469 444 R: TTTCGATAACTTCTTGATCCCTCTa 54.3 F: CTCGCACTAAGCTCGGAAATa 57.3 475 475 475 475 561 477 gcpm6 R: ACCATGGCGTTACTCTACCGa 53.9 F: TGGTGTGTTGAATCCACAATa 53.2 gcpm7 297 297 289 322 322 322 R: CCCCCTTTCCAATAATATCCAa 55.9 a F: TCCAAAGAGGAATCCTTCCA 53.3 gcpm8 237 237 237 313 237 237 R: CCAGCCTCTACTGGGGGTTAa 55.3 F: TCCAGGACTTCGAAAGGGTAa 53.4 gcpm9 492 492 492 492 486 511 R: ACACGATACCAAGGCAAACCa 53.7 F: CCGCTGTTATCCGCTACATTa 54.1 gcpm10 227 227 228 257 225 228 R: TCGTCTAAAATGCCTATACGAACTCa 54.9 F: CTGGACGATCCTATTTGGTCAb 53.7 gcpm11 220 220 220 238 220 202 R: TCCAGCTCCGTATGAAGGTCb 53.8 b F: GCAGAATACCGTCACCCATT 53.6 gcpm12 316 373 259 373 259 202 R: ATTTTGTCCGGATCCTCCTTb 53.8 F: AAGATTTTTATGAAGATACCGAAAATa 52.5 gcpm13 484 484 466 461 456 465 R: CGGTCAAATTCGAGGAAAGAa 55.3 F: TGGTTAGTTTCACCGGATTCAb 54.2 208 208 208 208 208 178 gcpm14 R: TTTTTGAGCCCATTTTTAAGGAb 54.6 Abbreviations: PCR, polymerase chain reaction; PgCP, Panax ginseng cv. CP; PgYP, P. ginseng cv. YP; Pq, P. quinquefolius; Pn, P. notoginseng; Pj, P. japonicus; Pv, P. vietnamensis. a Primers developed in our previous study17, and bprimers developed in this study Marker name

Forward (F)/reverse (R) primers

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Table 4. Marker combinations for each Panax species. Marker

Positions Regions CDS/IGS

PgCP

Allele types for each species PgYP Pq Pn Pj

Pv

trnK-UUU–rps16 IGS C C C D B A rps16–trnQ-UUG IGS A A B B B B atpH-atpI IGS B B B A B B atpH-atpI IGS B B A B B B trnE-trnT IGS B B B B A C trnE-trnT IGS B B B B A B rbcL-accD IGS B B C A A A petA-psbJ IGS B B B A B B clpP-psbB IGS B B B B B A rpl14–rpl16 IGS B B B A B B ycf2 CDS B B B A B C ycf1 CDS B A C AD C D ndhF–rpl32 IGS A A B C D C ycf1 CDS A A A A A B Abbreviations: CDS, coding sequences; IGS, intergenic spaces; PgCP, P. ginseng cv. CP; PgYP, P. ginseng cv. YP; Pq, P. quinquefolius; Pn, P. notoginseng; Pj, P. japonicus; Pv, P. vietnamensis. A, B, C, and D refer to different allele types.

gcpm1 gcpm2 gcpm3 gcpm4 gcpm5 gcpm6 gcpm7 gcpm8 gcpm9 gcpm10 gcpm11 gcpm12 gcpm13 gcpm14

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