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DNA barcoding: a genomic-based tool for

authentication of phytomedicinals and its products
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Botanics: Targets and Therapy
9 December 2015
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Karpaga Raja Sundari Abstract: DNA barcoding helps to identify the plant materials based on short, standardized
Balachandran gene sequences in a rapid, accurate, and cost-effective manner. Recent reports reveal that DNA
Saravanan Mohanasundaram barcoding can be used for the assignment of unknown specimens to a taxonomic group, authentic
Sathishkumar Ramalingam identification of phytomedicinals, and in plant biodiversity conservation. Research indicates
For personal use only.

that there is no single universal barcode candidate for identification of all plant groups. Hence,
Plant Genetic Engineering Laboratory,
Department of Biotechnology, comparative analysis of plant barcode loci is essential for choosing a best candidate for authen-
Bharathiar University, Coimbatore, ticating particular medicinal plant genus/families. Currently, both chloroplast/nuclear regions
Tamil Nadu, India are used as universal barcodes for the authentication of phytomedicinals. A recent advance in
genomics has further enhanced the progress in DNA barcoding of plants by the introduction
of high-throughput techniques like next generation sequencing, which has paved the way for
complete plastome sequencing that is now termed as super-barcodes. These approaches could
improve the traditional ethno-botanical and scientific knowledge of phytomedicinals and their
safe use. Hence, current focus is on the investigation of phytomedicinals and herbal product
integrity and authenticity through DNA barcoding with the goal of protecting consumers from
potential health risks associated with product substitution and contamination.
Keywords: phytomedicinals, DNA barcoding, NGS, super-barcodes, authentication, ethno-
genetics

Introduction
DNA barcoding is a technique that is used to identify the species based on species-
specific differences in short regions of their DNA.1 DNA barcoding uses state-of-the-art
biotechnology to identify plant species in a rapid, accurate, and cost-effective manner.
This technique is not restricted by morphological characteristics, physiological condi-
tions, and allows species identification without specialist taxonomic knowledge. This
has made researchers to use DNA barcoding technique to evaluate the herbal product
authenticity.
DNA barcoding uses the data of one or a couple of regions in the genome to
recognize all the species in a particular class.2 This technique opened up new doors
for DNA-based examinations extending from group phylogenetics to environmental
genomics.3,4 It has been reported that DNA barcoding is not only used to build phylo-
Correspondence: Sathishkumar genetic trees, but to provide rapid and accurate identification of unknown organisms.
Ramalingam Ideally, a DNA barcode should allow unambiguous species identification by having
Plant Genetic Engineering Laboratory,
Department of Biotechnology, Bharathiar
sufficient sequence variation between the species. This is an efficient tool to identify
University, Marudamalai Main Road, the species because levels of divergence among individuals of the same species are
Coimbatore-641 046, Tamil Nadu, India
Tel +91 93 6015 1669
usually much lower than the closely-related species that exhibit a “barcoding gap”
Email rsathish@[Link] between inter- versus intraspecific divergences.5

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Although the traditional DNA barcoding techniques + matK became the preferred choice and core barcodes.11
remain an effective method for identification of medicinal At the same time, the spacer between tRNA-His and
plants, the more advanced and newly developed high- photosystem II protein D1 (psbA-trnH spacer) and second
throughput sequencing techniques like next generation internal transcribed spacer (ITS2) were also widely used in
sequencing (NGS) technologies are potentially revolution- Vitaceae and Asteraceae families.12–14
izing this process.6 DNA barcoding usually targets short
regions of DNA molecule within the genome and does not Implication of genomic tools in
require full genome-scale data. DNA barcode-based NGS DNA barcoding technique
identifies the multiple plant species present in herbal product In recent years, genomic approaches have been introduced
admixtures, which has further modernized the method through in DNA barcoding technology. Many recent papers on DNA
multiplexing of different plant composite samples in a single barcoding in plants have been published.7,8 Due to these
step amplicon sequencing.7 Hence, the NGS approach has advances in DNA barcoding technique, multiple applica-
been introduced recently in DNA barcoding research. tions like ecological surveys, cryptic taxon identification,
authenticaion of phytomedicinals, and herbal drugs have
Molecular art behind DNA been employed.17,18 These applications can be extended
barcoding further if new genomic technologies are introduced into
The identification of the biological specimens using short this technique.
DNA sequences from either nuclear or organelle genomes is
called DNA barcoding. The term “DNA barcode” as a taxon Next generation DNA barcoding in
identifier was first proposed by Paul Hebert of University
phytomedicinals
of Guelph.1 Barcoding works by matching sequence data
Rapid advances in NGS technology are driving down the cost
from a query sample (an unknown specimen) to a reference
of sequencing and bringing large-scale sequencing projects
sequence (from a voucher specimen).
feasible by the individual investigators.19 Sample preparation
Initial in silico and laboratory-based assessment of dif-
has been regarded as the key factor in multiplex sequencing
ferent loci from chloroplast (cp) and nuclear genomes led
(sequencing of multiple tagged samples together in one lane)
to the conclusion that no single locus universal plant DNA
of plastid genomes. The application of NGS approach in DNA
barcode exists, and soon it was realized that multilocus
barcoding of plants has been extensively reviewed.20
DNA barcodes are required for plants.8 The Consortium for the
It has been recently reported that NGS provides useful and
Barcode of Life (CBOL), Plant Working Group (2009) evalu-
efficient workflow to identify pollen at the genus and species
ated seven cp genomic regions across the plant kingdom and
levels without requiring specialized palynological expert
proposed a combination of maturase K (matK) and ribulose 1,
knowledge.21 Another report on biological ingredient analysis
5-bisphosphate carboxylase/oxygenase large subunit (rbcL) as
of traditional Chinese medicine through high-throughput
plant barcodes. High universality and less species resolution
sequencing and metagenomic analysis revealed the use of
are provided by rbcL, whereas matK affords high resolution
potential candidates like ITS2 and trnL for the reliable iden-
and less universality. Hence, a combination of these two can
tification of phytomedicinals and their contaminants.22
help to achieve maximum species discrimination. However,
in closely-related species, the discriminating ability of these
two markers has been found to be very low.9 Therefore, the Super-barcoding: a recent genomic
addition of nuclear internal transcribed spacer (ITS) to the tool for plant discrimination
matK + rbcL combination was proposed as plant DNA barcode Recent reports reveal that the complete cp-genome contained
in order to achieve maximum identification efficiency even as much variation as the CO1 locus in animals and may be
between the closely-related species.10 used as a plant barcode.23,24 Currently, DNA barcoding tech-
At the Fourth International Barcode of Life Confer- nology relies heavily on cp loci because of their relatively low
ence ([Link] held in Adelaide, evolutionary rates as compared to the nuclear loci.25 These
Australia, the option of a three-locus barcode (matK + cp regions are potentially used in phylogenetic analyses. The
rbcL + psbA-trnH) versus a two-locus barcode was dis- use of cp-genome as a marker helps to overcome disputes
cussed. The two-locus barcode was preferred to avoid the with gene deletion, low polymerase chain reaction (PCR)
increased costs of sequencing, so the combination of rbcL efficiency,26 and also used efficiently to distinguish between

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 Dovepress Authentication of phytomedicinals by DNA barcoding

the closely-related species.27 The cp region provides a barcode Authentication of phytomedicinal

that can be effectively implemented to study the associations admixtures
in specific plant groups.28,29 Recent reports prove that herbal plants can be authenticated
As sequencing technology and bioinformatics continue using the barcode candidates in order to identify the contami-
to advance, complete plastome sequencing has revolu- nants among them. An extensive study has been conducted
tionized the technique of barcoding, which is termed as to analyze .6,600 plant samples belonging to 4,800 species
“Super-barcodes”.23 These plastid-genome-based species from 753 distinct genera using the genomic regions psbA-
classification and identification have been progressively trnH, matK, rbcL, rpoC1, ycf5, ITS, and ITS2. The results
accepted by taxonomists.28,29 The analysis of this super- suggested that the ITS2 of nuclear ribosomal DNA represents
barcode also resolved the problems of sequence retrieval the most suitable region for DNA barcoding applications in
usually encountered in traditional barcoding studies. Com- these plant samples.12 A recent review has revealed that there
pared with the nuclear genome, the cp-genome is small in are 17 potential barcode regions (matK, rbcL, ITS, ITS2,
size and has a higher interspecific and lower intraspecific psbA-trnH, atpF-atpH, ycf5, psbKI, psbM-trnD, coxI, nad1,
divergence, which makes it more suitable as a genome-based trnL-F, rpoB, rpoC1, atpF-atpH, and rps16) that aid in the
barcode.23 authentication and identification of phytomedicinals.7
Another report proved that DNA barcoding can efficiently
Application of DNA barcoding for authenticate the wholesomeness of medicinal plants that are
the analysis of phytomedicinals often used in Chinese herbal medicine. A total of 37 plants
People have developed trust on the use of natural components from 28 families were identified using rbcL as candidate
as a therapeutic agent due to fewer side effects. Hugely gene.38 DNA barcoding technique exhibits advantages over
popular Indian traditional medicinal systems like Ayurveda, chemical profiling because of its universal application includ-
Unani, and Homeopathy uses one or the other part of medici- ing the identification of unknown plant species. Recently, a
nal plants that have been recognized and accepted all over study was conducted to identify and authenticate selected
the world. The major problems to deal with phytomedicinals phytomedicinals commercially sold in Manila for predicting
are its correct identification and substitution of rare, expen- the most effective DNA barcodes using three cp markers
sive medicinal plants with the cheaper and easily available (psbA-trnH, matK, and rbcL) and a nuclear marker (ITS). This
ones.30 Hence, there is a need for the tool that gives correct study revealed that matK and psbA-trnH could be the potential
identification of plants at the molecular level. DNA barcoding barcodes for authenticating commercially sold medicinal
has been employed effectively as an ethno-genomics tool to plants, where morphological details are inadequate.39 The list
identify the cryptic species, phytomedicinals, and biological of commonly used DNA barcoding candidates for authentica-
authentication of materials that add value to both traditional tion of phytomedicinals has been summarized in Table 1.
ethno-botanical and scientific knowledge.31
The ITS barcode region has been used for the identifica- Herbal drug authentication by DNA
tion of medicinal plants at the molecular level including barcoding
medicinal plants of Selaginellaceae.12,32 DNA barcoding Herbal medicines have a widespread and well-documented
mainly depends on the genetic variation, the time requirement history of use in the prevention and treatment of various
for analysis, the cost/effectiveness ratio, and the technical diseases, which continue to gain global influence in mod-
expertise. Four DNA barcodes (rbcL, matK, psbA-trnH, and ern medical and health services. The international trade in
ITS2) have been successfully used in the identification of herbal products is a major force in the global economy and
many different species of phytomedicinals.33,34 Plant DNA the demand is increasing in both developing and developed
barcodes have been used efficiently to identify species rich- nations.34 Recent reports indicate that herbal products avail-
ness in unknown floras,35 identify traditional Tibetan medici- able to consumers in the market place may be contaminated
nal plant Gentianopsis paludosa,16 and discover complex or substituted with alternative plant species and ingredient
plant groups of Indian Berberis species.36 DNA barcoding substitutions that are not listed on the labels.17,54 A number
system has many prospective uses not only in the identi- of safety-related issues have emerged globally because of
fication but also in forensic science, verification of herbal the inaccurate identification of herbal materials. According
medicines, and foodstuffs, resolving ambiguity of species to the World Health Organization, adulteration of herbal
in plant systematics.37 products is causing an enormous threat to consumer safety.

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Table 1 Various DNA barcoding candidates used in the authentication of phytomedicinals

Medicinal plants Different barcode candidates Potential barcode identified Ref
analyzed for species authenticity
Scutellaria baicalensis (Lamiaceae) matK, rbcL, and psbA-trnH psbA-trnH 40
Datura metel ITS2, psbA-trnH, matK, and rbcL ITS2 or psbA-trnH 41
Datura innoxia
Datura stramonium
Brugmansia arborea (Solanaceae)
Boerhavia diffusa (Nyctaginaceae) ITS, ITS1, ITS2, and psbA-trnH ITS and ITS1 42
Colchicum autumnale rpoC1, psbA-trnH, matK, and ITS rpoC1, psbA-trnH, and ITS 43
Arlina brachylepis
Arundo donax (Colchicaceae, Armadillidiidae, and Poaceae)
Asparagus racemosus ITS2, matK, and rpoC1 ITS2 44
Hemidesmus indicus (Asparagaceae Apocynaceae)
Catharanthus roseus matK and psbA-trnH matK 45
Alstonia scholaris
Thevetia peruviana
Allamanda cathartica
Tabernaemontana divaricata
Calotropis gigantea (Rauvolfioideae)
Gentiana scabra rbcL, matK, ITS, and 5S rRNA 5S rRNA and trnL-F intergenic 46
Gentiana triflora intergenic spacer, chloroplast psbA- spacers
Gentiana manshurica and Gentiana rigescens (Gentianaceae) trnH , trnL-F and rpl36-rps8
Peucedanum No comparative analysis done ITS 47
praeruptorum (Apiaceae)
Crocus sativus (Iridaceae) No comparative analysis done psbA-trnH 48
Tulipa edulis (Liliaceae) matK, psbA-trnH, and rbcL matK 49
Ferula sinkiangensis No comparative analysis done ITS2 51
Ferula fukangensis (Apiaceae)
Thunbergia laurifolia Crotalaria spectabilis matK, rbcL, rpoC, and trnL High resolution melting analysis 52
(Acanthaceae and Fabaceae) using rpoC
Isatis tinctoria matK, rbcL, psbA-trnH, and ITS2 ITS2 53
Polygonum tinctorium
Strobilanthes cusia (Brassicaceae, Polygonaceae, and Acanthaceae)
Abbreviations: ITS, internal transcribed spacer; ITS2, second internal transcribed spacer; matK, maturase K; rbcL, ribulose 1, 5-bisphosphate carboxylase/oxygenase large subunit.

There are many reports on the ill-effects of herbal material large number and variety of medicinal plants species, which
due to the incorrect identification and adulteration of plant threatens patient safety and herbal efficacy.40
material.34,55–59 More recently, a universal publically available DNA
Herbal product substitution has been reported for many barcoding system for identifying herbal materials has been
individual plant species due to their morphological similarity established based on the ITS2, rbcL, matK, and psbA–trnH
like Echinacea sp., Chamomilla tincture,60 Phyllanthus,61,62 barcodes.17,43,68–71 There are only limited studies on the appli-
tea, 63 and nutraceuticals.64,65 Although there is limited cation of DNA barcoding to test natural products, which
research available, the frequency of product mislabeling in provide authentic assessment of commercial herbal products
herbal drugs has been estimated to be in the range from 14% within the marketplace. This includes reports on detecting
to 33%.54,66 There are legitimate health concerns for consum- adulteration through DNA barcoding for commercial tea
ers due to lack of confidence in the availability of safe and samples,63 black cohosh herbal dietary supplements,63 natu-
high quality herbal products. The immediate attention for ral health products,54 North American herbal drugs,17 and
achieving consumer confidence is driving the demand for adulterants in commercialized medicinal plant samples.72
research and market testing on herbal product authentication. Recently, NGS-based approach using ITS2 and trnL bar-
Traditional methods used to authenticate herbal materials codes have been attempted to identify biological ingredients
primarily include morphological, microscopic, and chemi- from herbal drugs of Chinese traditional medicine (Liuwei
cal identification.67 However, the ability to distinguish the Dihuang Wan) containing mixture of phytomedicinals.22
medicinal plants from their close relatives, inferior substi- DNA barcode identification can be applied to a wide
tutes, adulterants, and counterfeits presents a challenge to the range of herbal materials from the field, commercial trade,

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 Dovepress Authentication of phytomedicinals by DNA barcoding

and hospital pharmacy for authentication.33 DNA barcod- DNA barcode CBOL database. The National Center for
ing technology has a wide-reaching potential in the phy- Biotechnology Information web-based megablast algorithm
tomedicinal industry, especially to help ensure that herbal with default settings are used to identify the query sequences.
ingredients are correct and not contaminated or substituted. Each identification could be made manually by considering
Accurate species identification, resource monitoring, and E-value, maximum identity, and number of closely-related
quality control using DNA barcoding will soon become species represented in the database.43
an integral part of quality control workflow in herbal
industries.7 If the DNA barcoding result indicates that the BOLD, Canada
species is different from the intended plant prescribed on In order to make DNA barcoding information universally and
the label, then the use of this sample (and probably entire publically accessible, new databases have been made available
batch) should be avoided by which potential adverse reac- online. Rapid progress in DNA sequencing and computational
tions could be prevented.17 technologies made CBOL to build a universal organization for
Similarly, patented herbal products are increasingly popu- living beings inventory: the Barcode of Life Database (BOLD)
lar worldwide. However, they are prone to herbal substitution system. BOLD is created and maintained by the University of
and/or contamination because of the usage of conventional Guelph in Ontario, Canada ([Link] It
methods like phytochemical analysis, in which environmental facilitates researchers to collect, manage, and analyze DNA
factors can change the plant chemical profile drastically.54 barcode data. BOLD will provide a DNA barcode to clearly
In this situation, DNA barcoding could play an important identify the unknown specimens by facilitating accurate query
role in the authentication of the herbal products. This would assignments and by comparing the data that are obtained from
significantly decrease bio-safety issues and minimize the geographically dispersed institutions. BOLD could serve as the
trade of fake or incorrect herbs, which will ensure consumer universal starting point for species identification, which would
confidence.66 convey to the users to refer the specialized databases (eg, patho-
Currently, DNA barcode-based standard reference mate- genic strains, disease vector species, endangered species).74
rial library and standard testing procedures are being devel-
oped for commercial herbal species that could be integrated Medicinal Materials DNA Barcode
into cost-effective “best practices” in the manufacturing of database, People’s Republic of China
herbal products.7,17 A recent review on the authentication A dedicated DNA barcoding database was developed only
of herbal drug provides clear insight on DNA barcoding as for medicinal plant materials ([Link]
a standard method in herbal pharmacovigilance research.18 icm/[Link]), which accepts all plastid DNA regions
Another report suggests that DNA barcoding must be used and nuclear ITS results. Medicinal Materials DNA Barcode
in conjunction with metabolomics and need-based tran- ([Link] is a website that
scriptomics and proteomics for resolving authentication contains DNA sequences, their information, and important
challenges associated with the phytomedicinals in herbal references of medicinal records of the pharmacopoeia of
drugs.73 Hence, the DNA barcoding approach can support the People’s Republic of China, American Herbal Pharma-
immensely the herbal product authentication. copoeia, and other related references. Medicinal Materials
DNA Barcode database gives information on distinguishing
Sequence repositories and medicinal materials (plant, animal, and fungi) from their
consortia involved in plant common substitutes and adulterants.75
DNA barcoding
There are currently three barcode databases available for Consortia for plant DNA barcoding
plants that encompass the barcode sequences. CBOL
CBOL is an international initiative dedicated to developing
GenBank, USA DNA barcoding as a global standard for the identification of
The International Nucleotide Sequence Database work biological species.74 It was established in 2004 through support
together with GenBank in USA, European Molecular Biol- from the Alfred P Sloan Foundation, USA. CBOL promotes
ogy Laboratory in Germany, and DNA Data Bank of Japan barcoding through working groups, networks, workshops,
for DNA sequences. These databases regularly exchange conferences, outreach, and training. CBOL has 200 member
the DNA barcode sequence information with the dedicated organizations from 50 countries and promotes the exploration

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 Balachandran et al Dovepress

and development of DNA barcoding for species identifica- extracts, ancient samples, and old herbarium DNA samples.78
tion. It facilitates the rapid compilation of high quality DNA As a result, methods to sequence and analyze such material
barcode records in a public library of DNA sequences. typically would lead to false negative results. Hence, “specific
DNA authentication” methods are adopted recently using a
International Barcode of Life mini-barcode strategy, which targets small barcode regions
The International Barcode of Life project is the largest of fragmented DNA (∼100–200 bases in length) for botanical
biodiversity genomics initiative project with hundreds of extracts, oil, and tinctures.79,80 Some reports also reveal that
biodiversity scientists, genomics specialists, technologists, DNA barcoding method is not capable of determining the
and ethicists from 25 nations to construct a richly parameter- chemical constituents or plant parts of processed products
ized DNA barcode reference library ([Link] This and also for quantifying the amount of plant material used
library will be the foundation for a DNA-based identifica- in the product. Therefore, the use of additional methods (ie,
tion system for all multicellular life. There are 20 working microscopic and chemical) is necessary to verify the label
groups operating in five theme areas, which include DNA claims ensuring the safety and efficacy of the product. Hence,
Barcode library, Methods, Informatics, Technologies, and the use of multiple methods on processed materials is neces-
Administration. sary to increase the level of confidence in the identity and
quality of the material.81
China Plant Barcode of Life Group
The online DNA barcoding databases for herbal materials are Future prospects
being constructed by this group ([Link] DNA barcoding is being viewed as an integrated approach
which provides a species identification module for herbal with classical taxonomy for species identification and
materials. In this database, ITS2 and psbA-trnH are chosen authentication in the postgenomics era.30,82 DNA barcoding
as the core and supplementary DNA barcodes candidates for has been employed effectively to identify the cryptic spe-
medicinal herbs. This database also contains barcoding data cies, medicinal plants, species and biological authentica-
for their adulterants, substitutes, and closely-related species tion of materials, and plant biodiversity conservation that
in order to correctly distinguish the actual medicinal species. adds value to both traditional and scientific knowledge.31,83
This group provides access to online database and evaluates Contemporary approaches like ecological genomics along
the potential benefits of supplementing the core barcode for with the use of NGS could exploit and advance DNA barcod-
land plants.8 ing research to the next level. The barcoding movement along
with NGS approach could help to speed up the authentication
Limitations in DNA barcoding of voucher specimens and herbal drugs.
DNA barcoding in plants using combining multiple loci
approach has always been followed successfully. However, Acknowledgments
CBOL has focused on the identification of a universally KRSB thanks University Grants Commission–Dr D S Kothari
informative plant DNA barcode for the last several years, Post-Doctoral Fellowship, India, for the financial support. The
which could not be attained due to the complexity of plant authors would also like to thank DBT NER-Twining project
genome. The PCR success rate in barcoding regions is often for Junior Research Fellowship to SM, and UGC-SAP and
inhibited by the presence of secondary metabolites in plants. DST-FIST for the financial support.
These problems can be overcome by the modifications in
DNA extraction methods, primer sequences, and the use of
Disclosure
The authors report no conflicts of interest in this work.
an engineered polymerase enzyme.76 DNA barcoding can
be a significant tool for authentication of raw herbs, but its
application for finished herbal/botanical dietary supplements
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