DNA Mini-barcoding for wildlife trade control: a case study on identification of highly processed animal materials

The Quality Monitoring of Cistanches Herba (Cistanche deserticola Ma): A Value Chain Perspective

Cistanche deserticola Ma was used as a medicine food homology, which was mainly produced in the Alxa region of northwest China. In recent years, it has been widely used in various food items. The increasing demand for Cistanches Herba has led to problems such as overexploitation and quality deterioration. The quality and safety of herbal medicines are critical and have been shown to be affected by the value chain (VC). Using the VC framework, the study is embedded in a larger study aiming to investigate the effects of different VCs types on the quality and stakeholders of Cistanches Herba. In this study, 90 Cistanches Herba samples were collected during fieldwork. An additional 40 samples were obtained from the herbal markets and medicine purchasing stations. Semi-structured interviews and key informant interviews were performed to collect data on stakeholders in major production areas. These samples were analyzed using high performance liquid chromatography (HPLC) coupled with the k-means clustering method; a targeted quality assessment strategy based on chemical analysis was adopted to understand the quality of Cistanches Herba. Based on market research, the collected samples were divided into different grades through k-means clustering analysis. Moreover, quality differences of Cistanches Herba in Alxa region were explored through DNA barcoding and chemical analysis. Accordingly, 10 different types of VCs were determined in the production of Cistanches Herba. The results show that there is a close relationship between the quality of Cistanches Herba and stakeholder benefits. Vertical integration at different levels was found for independent farmer-based VCs, horizontal collaboration was found in the cooperative-based VCs. The vertical coordination has led to a more consistent traceability system and strict regulation of supply chains. At the same time, the Cistanches Herba were divided into three grades. Through DNA barcoding and chemical analysis, we found that the quality differences between Cistanches Herba in the Alxa area were not significant. It was found that geographical suitability and vertical integration could impact the quality and sustainable production of Cistanches Herba. At the same time, the well-developed VCs can provide products with reliable quality, and ensure adequate financial revenue for relevant stakeholders.

DNA-Based Authentication and Metabolomics Analysis of Medicinal Plants Samples by DNA Barcoding and Ultra-High-Performance Liquid Chromatography/Triple Quadrupole Mass Spectrometry (UHPLC-MS)

There is growing interest for medicinal plants in the world drug market. Particularly, Matricaria recutita L., Valeriana officinalis L., Tilia spp., and Camellia sinensis (L.) Kuntze are some of the most consumed medicinal plants for treatment of minor health problems. Medicinal plants are seen as natural and safe; however, they can cause interactions and produce adverse reactions. Moreover, there is lack of consensus in medicinal plants regulation worldwide. DNA barcoding and UHPLC-MS technique are increasingly used to correctly identify medicinal plants and guarantee their quality and therapeutic safety. We analyzed 33 samples of valerian, linden, tea, and chamomile acquired in pharmacies, supermarkets, and herbal shops by DNA barcoding and UHPLC-MS. DNA barcoding, using matk as a barcode marker, revealed that CH1 sold as Camellia sinensis was Blepharocalyx tweediei, and sample TS2 sold as linden belong to Malvales. On the other hand, UHPLC-MS analysis revealed the presence of bioactive compounds (apigenin-7-glucoside, acetoxy valerenic acid, valerenic acid, epigallocatechin, and tiliroside). However, none of samples met minimum content of these active principles (except for valerenic acid in VF3) according to the European Medicines Agency (EMA) and Real Spanish Pharmacopeia. In conclusion, this study revealed the need to incorporate DNA barcoding and HPLC-MS techniques in quality controls of medicinal plants.

Specific DNA mini-barcoding for identification of Gekko gecko and its products

Background

The dry body of the Tokay Gecko (Gekko gecko) is the source of a valuable traditional Chinese medicine, it is therefore listed as a Class II protected animal species in China. Due to increasing market demand and a declining supply of the species, a considerable number of adulterants have emerged in the market. Thus, it is necessary to establish an accurate and rapid method of identification for distinguishing G. gecko from its adulterants and for separating it from highly processed products.

Methods

A total of 274 COI sequences were analyzed by using MEGA 5.0 software. Several specific primers were designed to amplify mini-barcode regions and identify G. gecko from its counterfeits and products.

Results

274 COI sequences of G. gecko and 15 adulterants species were analyzed. G. gecko could be distinguished from its adulterants through BLAST analysis, intra- and inter-specific distance analyses, and an NJ tree based on COI sequences. Two pairs of specific primers designed for this study, COISF2/COISR2 and COISF3/COISR3, amplified 200- and 133-bp fragments of the COI region, respectively, both of which were suitable for the identification of G. gecko and its adulterants. Furthermore, COISF3/COISR3 detected G. gecko in 15 batches of products.

Conclusion

Therefore, the specific DNA mini-barcoding method developed here may be a powerful tool for the identification of G. gecko and counterfeits, and may also be used to distinguish G. gecko from its highly processed by-products.

DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry

Precious coral species have been used to produce jewelry and ornaments since antiquity. Due to the high value and demand for corals, some coral beds have been heavily fished over past centuries. Fishing and international trade regulations were put in place to regulate fishing practices in recent decades. To this date, the control of precious coral exploitation and enforcement of trade rules have been somewhat impaired by the fact that different species of worked coral samples can be extremely difficult to distinguish, even for trained experts. Here, we developed methods to use DNA recovered from precious coral samples worked for jewelry to identify their species. We evaluated purity and quantity of DNA extracted using five different techniques. Then, a minimally invasive sampling protocol was tested, which allowed genetic analysis without compromising the value of the worked coral objects.The best performing DNA extraction technique applies decalcification of the skeletal material with EDTA in the presence of laurylsarcosyl and proteinase, and purification of the DNA with a commercial silica membrane. This method yielded pure DNA in all cases using 100 mg coral material and in over half of the cases when using "quasi non-destructive" sampling with sampled material amounts as low as 2.3 mg. Sequence data of the recovered DNA gave an indication that the range of precious coral species present in the trade is broader than previously anticipated.

Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?

In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

Illegal product manufacturing and exportation from Pakistan: Revealing the factuality of highly processed wildlife skin samples via DNA mini-barcoding

Illegal trade is a major threat to the biodiversity and the efforts initiated for the conservation of wildlife. The shortcomings of the traditional taxonomic identification methods have been coped by a revolutionary and emerging technique, the "DNA (Deoxyribonucleic Acid) barcoding". Here we report a case of trader who was allegedly making footwear for a famous international celebrity from wild animal cutis. The samples confiscated during a raid on a footwear manufacturing industry by KP Wildlife department in August, 2016, were received by Bioresource Research Centre (BRC) for molecular identification on 1^st September, 2016. The study costed about USD 88 from processing to the identification of the samples. The samples identified via DNA mini-barcoding by targeting cytochrome oxidase I (COI) gene belong to Gazella bennettii and Bos taurus. Such studies are helpful for credible investigations that only lead to effective prosecution and control of illegal wildlife trade ultimately helping in conservation of wild animals.

Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication

INTRODUCTION

Herbal medicines play an important role globally in the health care sector and in industrialised countries they are often considered as an alternative to mono-substance medicines. Current quality and authentication assessment methods rely mainly on morphology and analytical phytochemistry-based methods detailed in pharmacopoeias. Herbal products however are often highly processed with numerous ingredients, and even if these analytical methods are accurate for quality control of specific lead or marker compounds, they are of limited suitability for the authentication of biological ingredients.

OBJECTIVE

To review the benefits and limitations of DNA barcoding and metabarcoding in complementing current herbal product authentication.

METHOD

Recent literature relating to DNA based authentication of medicinal plants, herbal medicines and products are summarised to provide a basic understanding of how DNA barcoding and metabarcoding can be applied to this field.

RESULTS

Different methods of quality control and authentication have varying resolution and usefulness along the value chain of these products. DNA barcoding can be used for authenticating products based on single herbal ingredients and DNA metabarcoding for assessment of species diversity in processed products, and both methods should be used in combination with appropriate hyphenated chemical methods for quality control.

CONCLUSIONS

DNA barcoding and metabarcoding have potential in the context of quality control of both well and poorly regulated supply systems. Standardisation of protocols for DNA barcoding and DNA sequence-based identification are necessary before DNA-based biological methods can be implemented as routine analytical approaches and approved by the competent authorities for use in regulated procedures. © 2017 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd.

Genetic identification for prey birds of the Endangered peregrine falcon (Falco peregrinus)

To reveal the dietary ecology of the peregrine falcon (Falco peregrinus), we conducted a molecular analysis for mitochondrial genes (COI and CYTB) to identify the prey species collected from a feeding place found on Sasu Island, South Korea. The results from noninvasive genetic analysis showed that the sequences obtained came from nine species of birds (Cuculus canorus, Eurystomus orientalis, Limosa limosa, Microscelis amaurotis, Oriolus chinensis, Phasianus colchicus, Sterna hirundo, Streptopelia orientalis, and Turdus pallidus). Five of the species (C. canorus, M. amaurotis, S. hirundo, S. orientalis, and T. pallidus) had previously been observed on this island, but the other four species (E. orientalis, L. limosa, O. chinensis, and P. colchicus) were newly identified as present. No mtDNA sequences of land animals such as amphibians, reptiles, and mammals were found in the dietary remains, suggesting that the peregrine falcon preys mostly on other birds rather than on other animals inhabiting Sasu Island. This island has rich avian diversity and abundant animal populations and therefore supplies sufficient dietary resources for the peregrine falcon. Our findings suggested that a DNA-based molecular method may be useful to identify the prey species of these birds and may be valuable in future studies of the Endangered peregrine falcon.