DNA barcoding,microarrays and next generation sequencing: recent tools for genetic diversity estimation and authentication of medicinal plants

DNA barcoding, microarray technology and next generation sequencing have emerged as promising tools for the elucidation of plant genetic diversity and its conservation. They are proving to be immensely helpful in authenticating the useful medicinal plants for herbal drug preparations. These newer versions of molecular markers utilize short genetic markers in the genome to characterize the organism to a particular species. This has the potential not only to classify the known and yet unknown species but also has a promising future to link the medicinally important plants according to their properties. The newer trends being followed in DNA chips and barcoding pave the way for a future with many different possibilities. Several of these possibilities might be: characterization of unknown species in a considerably less time than usual, identification of newer medicinal properties possessed by the species and also updating the data of the already existing but unnoticed properties. This can assist us to cure many different diseases and will also generate novel opportunities in medicinal drug delivery and targeting.     

Identification of herbal medicinal materials using DNA barcodes

Herbal medicinal materials have been used worldwide for centuries to maintain health and to treat disease. However, adulteration of herbal medicines remains a major concern of users and industry for reasons of safety and efficacy. Identification of herbal medicinal materials by DNA technology has been widely applied,started from the mid-1990s. In recent years, DNA barcoding of global plant species using four standard barcodes (rbcL, matK, trnH-psbA and ITS) has been a major focus in the fields of biodiversity and conservation. These DNA barcodes can also be used as reliable tools to facilitate the identification of herbal medicinal materials for the safe use of herbs, quality control, and forensic investigation. Many studies have applied these DNA barcodes for the identification of herbal medicinal species and their adulterants. The present article reviews efforts in the identification of herbal medicinal materials using the standard DNA barcodes and other DNA sequence-based markers.     

Bar-HRM for Authentication of Plant-Based Medicines: Evaluation of Three Medicinal Products Derived from Acanthaceae Species

Medicinal plants are used as a popular alternative to synthetic drugs, both in developed and developing countries. The economic importance of the herbal and natural supplement industry is increasing every year. As the herbal industry grows, consumer safety is one issue that cannot be overlooked. Herbal products in Thai local markets are commonly sold without packaging or labels. Plant powders are stored in large bags or boxes, and therefore buying local herbal products poses a high risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate three medicinal Acanthaceae species (Acanthus ebracteatus, Andrographis paniculata and Rhinacanthus nasutus) commonly used in Thailand. The rbcL barcode was selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Melting data from the HRM assay using the designed rbcL primers showed that the three chosen species could be distinguished from each other. HRM curves of all fifteen test samples indicated that three of tested products did not contain the indicated species. Two closely related species (A. paniculata and R. nasutus), which have a high level of morphological similarity, were interchanged with one another in three tested products. Incorrect information on packaging and labels of the tested herbal products was the cause of the results shown here. Morphological similarity among the species of interest also hindered the collection process. The Bar-HRM method developed here proved useful in aiding in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.     

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

Background

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over.

Methodology/Principal Findings

Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level.

Conclusions

The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.     

Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences

Background

Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.

Methodology/Principal Findings

Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants.

Conclusions/Significance

Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve existing discrepancies in phylogenetics and fingerprinting of plants.     

The Safety Assessment of Toxic Metals in Commonly Used Pharmaceutical Herbal Products and Traditional Herbs for Infants in Jordanian Market

The objective of this study was to assess the levels of contamination by toxic metals (Pb, Al, Ni, Cd and As) that may be present in 25 infant pharmaceutical herbal products and 15 traditional herbs in Jordan. Both products and medicinal herbs are currently prescribed by paediatricians. They are available as over-the-counter medicines and are sold the in herbal market, ensuring easy accessibility for parents. Inductively coupled plasma-optical emission spectroscopy (ICP-OES), with limit of detections (LODs) of 0.10, 1.00, 0.20, 0.15 and 2.00 mg.kg⁻¹ for Pb, Al, Ni, Cd and As respectively, was employed to measure the levels of toxic metals in the samples. Pb, Al and Ni were detected in 88, 76 and 4% of the analysed samples of pharmaceutical herbal products and in 93, 87 and 13% of the analysed samples of traditional herbs, respectively. Neither Cd or As were detected in all analysed samples. The data obtained were subsequently compared by referral to the acceptable limits of toxic heavy metals according to World Health Organisation (WHO) standards. Largely, the results showed acceptable toxic metal levels in the finished pharmaceutical products and the traditional medicinal herbs for infants. One exception to this was Persian Thyme (Satureja thymbra) with Pb content of 41.18 mg.kg⁻¹. Also, the daily intake of detected metals through pharmaceutical herbal products was found to be lower than the daily tolerable intake limit set by the regulatory bodies, except of 8% of products that exceeded the tolerable daily intake of Pb set by US FDA, as compared to traditional medicinal herbs, where the tolerable daily intake for Pb, Al and Ni were exceeded in 40, 60 and 8% of the analysed herbs, respectively. The results obtained revealed that the excessive use of medicinal plants as alternative medicine should be used with caution keeping in mind the safety factor in infants.

     

Investigation of the biosynthetic potential of endophytes in traditional Chinese anticancer herbs

Traditional Chinese medicine encompasses a rich empirical knowledge of the use of plants for the treatment of disease. In addition, the microorganisms associated with medicinal plants are also of interest as the producers of the compounds responsible for the observed plant bioactivity. The present study has pioneered the use of genetic screening to assess the potential of endophytes to synthesize bioactive compounds, as indicated by the presence of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes. The total DNA extracts of 30 traditional Chinese herbs, were screened for functional genes involved in the biosynthesis of bioactive compounds. The four PCR screens were successful in targeting four bacterial PKS, six bacterial NRPS, ten fungal PKS and three fungal NRPS gene fragments. Analysis of the detected endophyte gene fragments afforded consideration of the possible bioactivity of the natural products produced by endophytes in medicinal herbs. This investigation describes a rapid method for the initial screening of medicinal herbs and has highlighted a subset of those plants that host endophytes with biosynthetic potential. These selected plants can be the focus of more comprehensive endophyte isolation and natural product studies.     

Plant folk medicines among Nicobarese tribals of Car Nicobar Island,India

The present paper deals with investigations of less known medicinal plant lore among the aboriginal Nicobarese tribe of Car Nicobar island, India. Information on 73 species and their therapeutic applications and manner of use are initially documented and described as remedies in folkloric tradition and popular domestic medicine. No chemical principles are identified; no putative herbal remedies are pharmaceutically and medically evaluated. The aim of this paper is to gather information concerning medicinal plants and to provide access to specialists in search of their applications in modern medicine. A brief account of geography, climate, ethnology, and methodology adopted is given. Vernacular name(s) of the plants in the Nicobarese language are incorporated for the first time in the literature.     

Arbuscular mycorrhizal symbiosis and active ingredients of medicinal plants: current research status and prospectives

Medicinal plants have been used world-wide for thousands of years and are widely recognized as having high healing but minor toxic side effects. The scarcity and increasing demand for medicinal plants and their products have promoted the development of artificial cultivation of medicinal plants. Currently, one of the prominent issues in medicinal cultivation systems is the unstable quality of the products. Arbuscular mycorrhiza (AM) affects secondary metabolism and the production of active ingredients of medicinal plants and thus influence the quality of herbal medicines. In this review, we have assembled, analyzed, and summarized the effects of AM symbioses on secondary metabolites of medicinal plants. We conclude that symbiosis of AM is conducive to favorable characteristics of medicinal plants, by improving the production and accumulation of important active ingredients of medicinal plants such as terpenes, phenols, and alkaloids, optimizing the composition of different active ingredients in medicinal plants and ultimately improving the quality of herbal materials. We are convinced that the AM symbiosis will benefit the cultivation of medicinal plants and improve the total yield and quality of herbal materials. Through this review, we hope to draw attention to the status and prospects of, and arouse more interest in, the research field of medicinal plants and mycorrhiza.     

Novel antiviral agents: a medicinal plant perspective

Several hundred plant and herb species that have potential as novel antiviral agents have been studied, with surprisingly little overlap. A wide variety of active phytochemicals, including the flavonoids, terpenoids, lignans, sulphides, polyphenolics, coumarins, saponins, furyl compounds, alkaloids, polyines, thiophenes, proteins and peptides have been identified. Some volatile essential oils of commonly used culinary herbs, spices and herbal teas have also exhibited a high level of antiviral activity. However, given the few classes of compounds investigated, most of the pharmacopoeia of compounds in medicinal plants with antiviral activity is still not known. Several of these phytochemicals have complementary and overlapping mechanisms of action, including antiviral effects by either inhibiting the formation of viral DNA or RNA or inhibiting the activity of viral reproduction. Assay methods to determine antiviral activity include multiple-arm trials, randomized crossover studies, and more compromised designs such as nonrandomized crossovers and pre- and post-treatment analyses. Methods are needed to link antiviral efficacy/potency- and laboratory-based research. Nevertheless, the relative success achieved recently using medicinal plant/herb extracts of various species that are capable of acting therapeutically in various viral infections has raised optimism about the future of phyto-antiviral agents. As this review illustrates, there are innumerable potentially useful medicinal plants and herbs waiting to be evaluated and exploited for therapeutic applications against genetically and functionally diverse viruses families such as Retroviridae, Hepadnaviridae and Herpesviridae     

Culturable Endophytes of Medicinal Plants and the Genetic Basis for Their Bioactivity

The bioactive compounds of medicinal plants are products of the plant itself or of endophytes living inside the plant. Endophytes isolated from eight different anticancer plants collected in Yunnan, China, were characterized by diverse 16S and 18S rRNA gene phylogenies. A functional gene-based molecular screening strategy was used to target nonribosomal peptide synthetase (NRPS) and type I polyketide synthase (PKS) genes in endophytes. Bioinformatic analysis of these biosynthetic pathways facilitated inference of the potential bioactivity of endophyte natural products, suggesting that the isolated endophytes are capable of producing a plethora of secondary metabolites. All of the endophyte culture broth extracts demonstrated antiproliferative effects in at least one test assay, either cytotoxic, antibacterial or antifungal. From the perspective of natural product discovery, this study confirms the potential for endophytes from medicinal plants to produce anticancer, antibacterial and antifungal compounds. In addition, PKS and NRPS gene screening is a valuable method for screening isolates of biosynthetic potential.     

Herbal plants in the traditional medicine of Bahrain

Plant samples collected in Bahrain and data reported in the literature indicate the flora of Bahrain to contain 52 species (49 genera; 20 families) of medicinal interest. Of these plant species 20 appear to be indigenous and are being used in traditional herbal remedies for numerous afflictions. Preparation of such remedies appears to be simple and includes boiling, infusions, extraction of milled dry or fresh leaves, flowers, seeds or whole plants. Direct consumption of plant parts, raw or cooked, is also practiced. None of these plants has been studied systematically to evaluate their medicinal potential.     

Quantitative ethnobotany of medicinal plants uses in the Jhelum valley,Azad Kashmir,Pakistan

Indigenous knowledge provides information on phytotherapeutic potential of medicinal plants for basic health care mangements in local communinites. The present study was aimed to document folklore knowledge of ethnic communities, who are practicing the herbal medicines in the Jhelum valley (District Hattian), Azad Kashmir, Pakistan. The information regarding folklore use of plants was collected from local communities through informed consent semi- structured interviews from 152 key informants. The ethnobotanical data were quantitatively analyzed using indices of use value (UV), relative frequency citation (RFC) and Informant census factor (ICF). A total of 113 medicinal plant species belong to 52 families were documented in the local communites of Jhelum Valley. The Asteraceae and Polygonaceae were the dominant plant families. The plant species hold potential folklore uses against hepatitis, stomach and respiratory problems, tooth ache, skin ailments and tumor treatment. The whole plants (32.52%), leaves ((21.14%)) were highly consumed plant parts and decoction (22.99%), powder form (18.39%) and infusion (13.79%) was the commonly used method for herbal formulation. The species with maximum use value was Beberis lyceum (0.80) and Valeriana jatamansi (0.60). The highest ICF value was obtained for disease catergories that is ear pain (1.00) followed by heaptic disorder (0.94) and urinary system disorders (0.89). The lowest ICF value was recored for nervous system disorders (0.44). The present study disclosed that traditional knowledge of medicinal plants is still widespread in ethnic people, but gradually decline in youngers. Documentation of newly documented plant species with their folklore uses shall uphold further phytochemical and pharmacological studies.     

PCR-based rapid diagnostic tools for the authentication of medicinal mistletoe species

BackgroundTaxilli Herba (TH) and Visci Herba (VH), defined as the leaves and branches of the mistletoe species Taxillus chinensis and Viscum coloratum, respectively, are popular herbal medicines in East Asia. However, commercial TH and VH products are frequently adulterated with related inauthentic mistletoe species, posing efficacy and safety concerns. Accurate species identification of herbal medicinal products is a prerequisite for quality control, but traditional morphological identification methods are hampered by difficulties in discriminating among closely related species and in identifying the source materials in processed products.PurposeThis study aimed to develop sequence-characterized amplified region (SCAR) markers and a multiplex-SCAR assay for rapid and accurate identification of authentic TH and VH.MethodsThe matK region was sequenced in a total of 20 samples from five mistletoe species, namely T. chinensis and V. coloratum, and three species often found in adulterated herbal medicines, T. sutchuenensis, V. articulatum, and Macrosolen tricolor. Species-specific nucleotide polymorphisms were identified and short regions (21–22 bp) containing at least two species-specific nucleotides close to the 3ʹ end were incorporated into SCAR primers that produced uniquely sized PCR amplicons for each species. The five SCAR primer sets were also combined into a multiplex-SCAR assay.ResultsThe SCAR primers successfully generated amplicons of the expected size for each target species even with low-DNA templates or with templates containing DNA from multiple samples. No amplification was observed in non-target species. The SCAR markers and the multiplex-SCAR assay successfully identified commercial TH and VH products that were counterfeit or adulterated in both dried and processed products.ConclusionThis is the first report to illustrate discrimination of genuine medicinal mistletoe species with DNA-based marker assays, enabling rapid and accurate species identification. The SCAR assays developed in this study will facilitate the standardization of commercial mistletoe products.     

Sustainable Utilization and Economic Development of Some Plant Resources in Northern Pakistan

Overshadowed by the vast impact that habitat loss has on targeted plant species survival, it is easy to overlook the fact that utilization and harvesting of species can often result in their genetic depletion and in an often rapid downward trend of their population status. In this regard an ethnobotanical study on the medicinal plants of Shawar valley, District Swat was conducted with the aims to document medicinal plants and to examine the current status of the medicinal plants trade as well as the market chain starting from collectors to consumers. The survey reported 50 species of plants belonging to 33 families as ethnomedicinally important. These species were used as crud drugs by the local people and folk-lore for treating diseases in traditional system of medicine. The detailed local uses, recipe preparation along with their local names and diseases treated were recorded for each species.Market survey revealed that the structure of medicinal plant trade is complex and heterogeneous, involving many players. The collectors are often not aware of the high market prices and medicinal values, and most of the collected material is sold to local middlemen at a very low price. There was an increase of 3 to 5 folds in prices from collectors to the national market.Recommendations were given in the spheres of training sustainable harvesting and post harvesting of wild medicinal plant resources, trade monitoring, equitable sharing of benefits of wild resources, improved control on harvesting and trade for the conservation of resources, enhancement of cultivation efforts, future research into trade in wild harvested plants, community participation in natural resource management and value addition in the herbal products to maximize the benefits.     

An ethnobotanical survey of indigenous knowledge on medicinal plants used by the traditional healers of the Lwamondo area,Limpopo province,South Africa

The use of medicinal plants in the treatment and prevention of diseases is attracting the attention of scientists worldwide. Approximately 3000 plant species are currently used by an estimated 200,000 indigenous traditional healers in South Africa. The specific part of the plant used for medicinal applications varies from species to species, and from one traditional healer to another. This study was carried out to explore and record those plants and plant parts used for treating various human ailments by the traditional healers of the Lwamondo area in the Limpopo province, South Africa for medicinal purposes. Ethnobotanical data were collected from 30 traditional healers (24 females and 6 males) in the Lwamondo area of Venda, by means of a data capture questionnaire focusing on the local names of the medicinal plants, their medicinal uses, the plant parts used, and methods of preparation and of administering treatments to patients. The survey identified 16 medicinal plants from 7 families, with 14 genera, used to treat a range of ailments in the Lwamondo area. The Fabaceae family was the most commonly used plant family representing 43.8% of all the medicinal plants species recorded by this study, followed by the Varbenaceae family at 18.8%. The plant parts most frequently used were the roots (44.5%), followed by the leaves (25.9%), bark (14.8%), the whole plant (11%), and flowers (3.7%). Most of the traditional healers obtained their extracts by boiling the medicinal plants. The most often recurring ailment treated by healers was stomach problems, using 31.3% of all the medicinal plants reported in this study for preparing such treatments. The following medicinal plants were covered by this study: Annona senegalensis, Schkuhria pinnata, Diospyros mespiliformis, Piliostigma thonningii, Senna obtusifolia, Bauhinia galpinii. The rural communities of the Lwamondo area possess a wealth of information on medicinal plants and their applications. This ethnobotanical survey can help scientists identify for further research those plants whose medicinal properties may be useful in the development of new drugs.     

A renaissance in herbal medicine identification: From morphology to DNA

Numerous adverse reactions have arisen following the use of inaccurately identified medicinal plant ingredients, resulting in conditions such as aristolochic acid nephropathy and herb-induced poisoning. This problem has prompted increased global concern over the safety of herbal medicines. DNA barcoding, a technique aiming at detecting species-specific differences in a short region of DNA, provides a powerful new tool for addressing this problem. A preliminary system for DNA barcoding herbal materials has been established based on a two-locus combination of ITS2 + psbA–trnH barcodes. There are 78,847 sequences belonging to 23,262 species in the system, which include more than 95% of crude herbal drugs in pharmacopeia, such as those of China, Japan, Korea, India, USA, and Europe. The system has been widely used in traditional herbal medicine enterprises. This review summarizes recent key advances in the DNA barcoding of medicinal plant ingredients (herbal materia medica) as a contribution towards safe and efficacious herbal medicines.     

Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns

Traditional Chinese medicine (TCM) has been practiced for thousands of years, but only within the last few decades has its use become more widespread outside of Asia. Concerns continue to be raised about the efficacy, legality, and safety of many popular complementary alternative medicines, including TCMs. Ingredients of some TCMs are known to include derivatives of endangered, trade-restricted species of plants and animals, and therefore contravene the Convention on International Trade in Endangered Species (CITES) legislation. Chromatographic studies have detected the presence of heavy metals and plant toxins within some TCMs, and there are numerous cases of adverse reactions. It is in the interests of both biodiversity conservation and public safety that techniques are developed to screen medicinals like TCMs. Targeting both the p-loop region of the plastid trnL gene and the mitochondrial 16S ribosomal RNA gene, over 49,000 amplicon sequence reads were generated from 15 TCM samples presented in the form of powders, tablets, capsules, bile flakes, and herbal teas. Here we show that second-generation, high-throughput sequencing (HTS) of DNA represents an effective means to genetically audit organic ingredients within complex TCMs. Comparison of DNA sequence data to reference databases revealed the presence of 68 different plant families and included genera, such as Ephedra and Asarum, that are potentially toxic. Similarly, animal families were identified that include genera that are classified as vulnerable, endangered, or critically endangered, including Asiatic black bear (Ursus thibetanus) and Saiga antelope (Saiga tatarica). Bovidae, Cervidae, and Bufonidae DNA were also detected in many of the TCM samples and were rarely declared on the product packaging. This study demonstrates that deep sequencing via HTS is an efficient and cost-effective way to audit highly processed TCM products and will assist in monitoring their legality and safety especially when plant reference databases become better established.     

Does extraction of DNA and RNA by magnetic fishing work for diverse plant species?

An automated nucleic acid extraction procedure with magnetic particles originally designed for isolation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from animal tissues was tested for plant material. We isolated genomic DNA and total RNA from taxonomically diverse plant species representing conifers (Scots pine), broad-leaved trees (silver birch and hybrid aspen), dwarf shrubs (bilberry), and both monocotyledonous (regal lily) and dicotyledonous (Saint John's wort, round-leaved sundew, and tobacco) herbaceous plants. Buffers developed for DNA extraction were successfully used in addition to manufacturer's extraction kits. The quality of RNA was appropriate for many applications, but the quality of DNA was not always sufficient for polymerase chain reaction (PCR) amplification. However, we could strikingly improve the quality by eliminating the adherent compounds during the extraction or later in the PCR phase. Our results show that the use of the procedure could be extended to diverse plant species. This procedure is especially suitable for small sample sizes and for simultaneous processing of many samples enabling large-scale plant applications in population genetics, or in the screening of putative transgenic plants.