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Castro AA, Nunes R, Carvalho LR, Targueta CP, Dos Santos Braga-Ferreira R, de Melo-Ximenes AA, Corvalán LCJ, Bertoni BW, Pereira AMS, de Campos Telles MP. Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily. Sci Rep 2023; 13:8390. [PMID: 37225737 DOI: 10.1038/s41598-023-34334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.
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Affiliation(s)
- Andrezza Arantes Castro
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Rhewter Nunes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil.
- Instituto Federal de Goiás - Campus Cidade de Goiás (IFG), Goiás, GO, 74600-000, Brazil.
| | - Larissa Resende Carvalho
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Ramilla Dos Santos Braga-Ferreira
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Amanda Alves de Melo-Ximenes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Leonardo Carlos Jeronimo Corvalán
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | | | | | - Mariana Pires de Campos Telles
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás (PUC - GO), Goiânia, GO, 74605-050, Brazil
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Mahima K, Sunil Kumar KN, Rakhesh KV, Rajeswaran PS, Sharma A, Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Front Pharmacol 2022; 13:947512. [PMID: 36339543 PMCID: PMC9635000 DOI: 10.3389/fphar.2022.947512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023] Open
Abstract
Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
- Department of Pharmacognosy, Siddha Central Research Institute, Chennai, Tamil Nadu, India
| | | | | | | | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Santiago de Queretaro, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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3
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Jiang S, Chen F, Qin P, Xie H, Peng G, Li Y, Guo X. The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:837-848. [PMID: 35592487 PMCID: PMC9110604 DOI: 10.1007/s12298-022-01175-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 05/07/2023]
Abstract
UNLABELLED More than 600 species in over 40 genera have been identified in family Theaceae worldwide. The accurate identification of Theaceae plants can ensure the market economic order, and it plays a vital role in achieving the sustainable utilization of germplasm resources. DNA barcoding, one of the most potential species identification technologies at present, has advanced in the rapid, accurate and repetitive discrimination of species. In this study, matK + ndhF + ycf1 was observed as the optimal combined candidate gene sequence of DNA barcodes by analyzing genetic information of four single chloroplast DNA sequences, including matK, rbcL, ndhF and ycf1, as well as six combined gene sequences. Subsequently, the experiments were performed on phylogenetic analysis based on genetic distance to study the phylogenetic relationship of Theaceae plants and evaluate the species identification accuracy of matK + ndhF + ycf1. Lastly, the species-specific DNA barcodes were designed by searching the variable sites (one type of single nucleotide polymorphism sites) for the accurate identification of Camellia amplexicaulis, Franklinia alatamaha, Gordonia brandegeei and Stewartia micrantha. The previous methods of screening and testing candidate gene sequences were optimized, and innovation was made in the above methods. The process of making visual DNA barcodes was standardized. Besides, DNA barcoding technology increased the accuracy of species identification and DNA barcoding was analyzed in accordance with the theories of population genetics (e.g., neutral theory of molecular evolution). The results of the study will lay a basis for the identification and protection of Theaceae species and germplasm resources. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01175-7.
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Affiliation(s)
- Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082 China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082 China
| | - Pai Qin
- College of Biology, Hunan University, Changsha, 410082 China
| | - Hai Xie
- College of Biology, Hunan University, Changsha, 410082 China
| | - Guo Peng
- College of Biology, Hunan University, Changsha, 410082 China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082 China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082 China
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Avarave S, Thomas J. Biodiversity of South Indian tea clones with detection of plant-based adulterants in tea dust using DNA barcoding. Nat Prod Res 2021; 36:4614-4619. [PMID: 34847786 DOI: 10.1080/14786419.2021.2002325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Tea is by and large a highly penetrated product in south India. Hence the adulteration risk in tea dust gets hiked in the markets. We constructed a standard database using plant plastid markers (rbcL, matK, trnH-psbA, rpoC, rpoB, ycf 1) and nuclear (ITS2) locus from prominent south Indian tea clones representing Assam, China, and Cambod varieties. These barcodes were used as reference algorithm to investigate the authenticity of 10 sampled commercial tea dust by recovering its DNA barcodes using rbcL, matK, and ITS2 loci. PCR amplification success, sequencing efficiency, genetic polymorphisms, BLAST search, and phylogenetic analysis were performed to enhance genotypic information on south tea cultivars and in authenticating the commercial samples of Camellia sinensis. Findings suggest that the chloroplast and nuclear loci can identify tea plant at the genus and varietal level respectively and rbcL as the potential marker for detecting plant-based admixtures coupled with TA cloning after DNA barcoding.
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Affiliation(s)
- Steffi Avarave
- Algae Biomass Research Laboratory, Department of Biotechnology, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, Tamil Nadu, India
| | - Jibu Thomas
- Algae Biomass Research Laboratory, Department of Biotechnology, Karunya Institute of Technology and Sciences (Deemed to be University), Coimbatore, Tamil Nadu, India
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5
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Quantification of adulteration in traded ayurvedic raw drugs employing machine learning approaches with DNA barcode database. 3 Biotech 2021; 11:463. [PMID: 34745814 DOI: 10.1007/s13205-021-03001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022] Open
Abstract
Adulteration of expensive raw drugs with inferior taxa has become a routine practice, conceding the quality and safety of derived herbal products. In this regard, the study addresses the development of an integrated approach encompassing DNA barcode and HPTLC fingerprinting to authenticate chiefly traded ayurvedic raw drugs in south India [viz. Saraca asoca (Roxb.) Willd., Terminalia arjuna (Roxb. ex DC.) Wight and Arn., Sida alnifolia L. and Desmodium gangeticum (L.) DC.] from its adulterants. Consortium of Barcode of Life (CBOL) recommended DNA barcode gene regions viz. nuclear ribosomal-Internal Transcribed Spacer (nrDNA-ITS), maturase K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and psbA-trnH spacer regions along with HPTLC profiling were experimented and a reference database was created. Further, an integrated analytical approach employing genetic distance-based Maximum Likelihood phylogenetic tree and Artificial Intelligence (AI)based Machine Learning Algorithms (MLA)-Waikato Environment for Knowledge Analysis (WEKA) and Barcoding with Logic (BLOG) were employed to prove efficacy of DNA barcode tool. Even though, among the four barcodes, psbA-trnH (S. alnifolia and its adulterants, T. arjuna and its adulterants) or ITS region (S. asoca and its adulterants, D. gangeticum and its adulterants) showed highest inter specific divergences in the selected Biological Reference Materials (BRMs), rbcL or matK barcode regions alone were successful for authentication of traded samples. The automated species identification techniques, WEKA and BLOG, experimented for the first time in India for raw drug validation, could achieve rapid and precise identification. A national certification agency for raw drug authentication employing an integrated approach involving a DNA barcoding tool along with standard organoleptic and analytical methods can strengthen and ensure safety and quality of herbal medicines in India. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03001-5.
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6
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Paradiso L, Little DP. Authentication of garlic ( Allium sativum L.) supplements using a trnLUAA mini-barcode. Genome 2021; 64:1021-1028. [PMID: 34609923 DOI: 10.1139/gen-2021-0001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Garlic (Allium sativum), a widely distributed plant with great cultural and medicinal significance, is one of the most popular herbal dietary supplements in Europe and North America. Garlic supplements are consumed for a variety of reasons, including for their purported antihypertensive, antibacterial, and anticarcinogenic effects. The steady increase in the global herbal dietary supplement market paired with a global patchwork of regulatory frameworks makes the development of assays for authentication of these products increasingly important. A DNA mini-barcode assay was developed using the P6 loop of the plastid trnLUAA intron to positively identify A. sativum products. Analysis of 43 commercially available garlic herbal dietary supplements produced mini-barcode sequences for 33 supplements, all of which contained detectable amounts of A. sativum. The trnLUAA P6 mini-barcode can be highly useful for specimen identification, particularly for samples that may contain degraded DNA.
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Affiliation(s)
- Lydia Paradiso
- The New York Botanical Garden, Bronx, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Damon P Little
- The New York Botanical Garden, Bronx, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
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7
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Zhao P, Ji SP, Cheng XH, Bau T, Dong HX, Gao XX. DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms ( Pleurotus). Front Microbiol 2021; 12:624347. [PMID: 34093459 PMCID: PMC8176306 DOI: 10.3389/fmicb.2021.624347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/09/2021] [Indexed: 11/20/2022] Open
Abstract
Oyster mushrooms (genus Pleurotus) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. A total of 160 sequences of the candidate loci were analyzed. Intra- and interspecific divergences and the ease of nucleotide sequence acquisition were the criteria used to evaluate the candidate genes. EF-1α showed the best intra- and interspecific variation among the candidate markers and discriminated 84.6% of the species tested, only being unable to distinguish two closely related species Pleurotus citrinopileatus and Pleurotus cornucopiae. Furthermore, EF-1α was more likely to be acquired than ITS or 28S rDNA, with an 84% success rate of PCR amplification and sequencing. For ITS and 28S rDNA, the intraspecific differences of several species were distinctly larger than the interspecific differences, and the species identification efficiency of the two candidate markers was worse (61.5 and 46.2%, respectively). In addition, these markers had some sequencing problems, with 55 and 76% success rates of sequencing, respectively. Hence, we propose EF-1α as a possible DNA barcode marker for oyster mushroom spawn.
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Affiliation(s)
- Peng Zhao
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Sen-Peng Ji
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Xian-Hao Cheng
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Tolgor Bau
- Institute of Mycology, Jilin Agricultural University, Changchun, China
| | - Hong-Xin Dong
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Xing-Xi Gao
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
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8
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Jones L, Twyford AD, Ford CR, Rich TCG, Davies H, Forrest LL, Hart ML, McHaffie H, Brown MR, Hollingsworth PM, de Vere N. Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom. Mol Ecol Resour 2021; 21:2050-2062. [PMID: 33749162 DOI: 10.1111/1755-0998.13388] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/09/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding and metabarcoding provide new avenues for investigating biological systems. These techniques require well-curated reference libraries with extensive coverage. Generating an exhaustive national DNA barcode reference library can open up new avenues of research in ecology, evolution and conservation, yet few studies to date have created such a resource. In plant DNA barcoding, herbarium collections provide taxonomically robust material but also pose challenges in lab processing. Here, we present a national DNA barcoding resource covering all of the native flowering plants and conifers of the United Kingdom. This represents 1,482 plant species, with the majority of specimens (81%) sourced from herbaria. Using Sanger sequencing of the plant DNA barcode markers, rbcL, matK, and ITS2, at least one DNA barcode was retrieved from 98% of the UK flora. We sampled from multiple individuals, resulting in a species coverage for rbcL of 96% (4,477 sequences), 90% for matK (3,259 sequences) and 75% for ITS2 (2,585 sequences). Sequence recovery was lower for herbarium material compared to fresh collections, with the age of the specimen having a significant effect on the success of sequence recovery. Species level discrimination was highest with ITS2, however, the ability to successfully retrieve a sequence was lowest for this region. Analyses of the genetic distinctiveness of species across a complete flora showed DNA barcoding to be informative for all but the most taxonomically complex groups. The UK flora DNA barcode reference library provides an important resource for many applications that require plant identification from DNA.
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Affiliation(s)
- Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Alex D Twyford
- Royal Botanic Garden Edinburgh, Edinburgh, UK.,School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | - Col R Ford
- National Botanic Garden of Wales, Llanarthne, UK
| | | | | | | | | | | | - Max R Brown
- School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | | | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Unnikrishnan R, Sumod M, Jayaraj R, Sujanapal P, Dev SA. The efficacy of machine learning algorithm for raw drug authentication in Coscinium fenestratum (Gaertn.) Colebr. employing a DNA barcode database. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:605-617. [PMID: 33854287 PMCID: PMC7981360 DOI: 10.1007/s12298-021-00965-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 05/05/2023]
Abstract
Medicinal plants are a valuable resource for traditional as well as modern medicine. Consequently huge demand has exerted a heavy strain on the existing natural resources. Due to over exploitation and unscientific collection most of the commercially traded ayurvedic plants are in the phase of depletion. Adulteration of expensive raw drugs with inferior taxa has become a common practice to meet the annual demand of the ayurvedic industry. Although there are several recommended methods for proper identification varying from the traditional taxonomic to organoleptic and physiochemical, it is difficult to authenticate ayurvedic raw drugs available in extremely dried, powdered or shredded forms. In this regard, the study addresses proper authentication and illicit trade in Coscinium fenestratum (Gaertn.) Colebr. using CBOL recommended standard barcode regions viz. nuclear ribosomal-Internally Transcribed Spacer (nrDNA- ITS), maturase K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), and psbA-trnH spacer regions. Further, an integrated analytical approach employing Maximum Likelihood phylogenetic tree and Machine Learning Approach, Waikato Environment for Knowledge Analysis was employed to prove efficacy of the method. The automated species identification technique, Artificial Intelligence uses the ability of computers to build models that can receive the input data and then conduct statistical analyses which significantly reduces the human labour. Concurrently, scientific management, restoration, cultivation and conservation measures should be given utmost priority to reduce the depletion of wild resources as well as to meet the rapidly increasing demand of the herbal industries.
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Affiliation(s)
- Remya Unnikrishnan
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
- Cochin University of Science and Technology, Kochi, Kerala India
| | - M. Sumod
- Sustainable Forest Management Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
| | - R. Jayaraj
- Forest Ecology and Biodiversity Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
| | - P. Sujanapal
- Sustainable Forest Management Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
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10
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Nehal N, Choudhary B, Nagpure A, Gupta RK. DNA barcoding: a modern age tool for detection of adulteration in food. Crit Rev Biotechnol 2021; 41:767-791. [PMID: 33530758 DOI: 10.1080/07388551.2021.1874279] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Globalization of the food trade requires precise and exact information about the origin, methods of production, transformation technologies, authentication, and the traceability of foodstuffs. New challenges in food supply chains such as deliberate fraudulent substitution, tampering or mislabeling of food and its ingredients or food packaging incapacitates the market and eventually the national economy. Currently, no proper standards have been established for the authentication of most of the food materials. However, in order to control food fraud, various robust and cost-effective technologies have been employed, like a spectrophotometer, GC-MS, HPLC, and DNA barcoding. Among these techniques, DNA barcoding is a biotechnology advantage with the principle of using 400-800 bp long standardized unique DNA sequences of mitochondrial (e.g. COI) or plastidial (e.g. rbcL) of nuclear origin (e.g. ITS) to analyze and classify the food commodities. This review covers several traded food commodities like legumes, seafood, oils, herbal products, spices, fruits, cereals, meat, and their unique barcodes which are critically analyzed to detect adulteration or fraud. DNA barcoding is a global initiative and it is being accepted as a global standard/marker for species identification or authentication. The research laboratories and industries should collaborate to realize its potential in setting standards for quality assurance, quality control, and food safety for different food products.
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Affiliation(s)
- Nazish Nehal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, India
| | - Bharti Choudhary
- School of Studies in Biotechnology, Pt. Ravi Shankar Shukla University, Raipur, India
| | - Anand Nagpure
- Biology Division, State Forensic Science Laboratory, Bhopal, India
| | - Rajinder K Gupta
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
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11
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Oyebanji OO, Chukwuma EC, Bolarinwa KA, Adejobi OI, Adeyemi SB, Ayoola AO. Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers. J Biosci 2020. [DOI: 10.1007/s12038-020-00061-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Lagiotis G, Stavridou E, Bosmali I, Osathanunkul M, Haider N, Madesis P. Detection and quantification of cashew in commercial tea products using High Resolution Melting (HRM) analysis. J Food Sci 2020; 85:1629-1634. [PMID: 32468625 DOI: 10.1111/1750-3841.15138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/28/2020] [Accepted: 03/19/2020] [Indexed: 11/29/2022]
Abstract
Tea, a popular aromatic infusion and food supplement, prepared from Camellia sinensis (L.) Kuntze leaves, is often subjected to adulteration with various undeclared inorganic and plant-derived materials. Cashew (Anacardium occidentale L.) nut husk is one of the most common plant tea adulterants. To date, there are limited DNA-based technologies for tea authentication and quantitative detection of adulterants. Herein, we used a universal plant DNA barcoding marker coupled with High Resolution Melting (Bar-HRM) analysis to authenticate tea products from cashew ground nut. Additionally, cashew-specific markers coupled with HRM technology were used to detect and quantify adulteration of tea with cashew DNA. This methodology can reliably detect admixtures as low as 1% v/v cashew in commercial tea products. Overall, our results demonstrate that the HRM technology is a strong molecular approach in tea authentication, capable of detecting very low adulterations in DNA admixtures. PRACTICAL APPLICATION: In this study, we established the use of high-resolution DNA-based technologies for the detection of cashew adulteration in tea, even in very low quantities. The technology could be applied to a greater range of plant-based tea adulterants. This work is expected to facilitate the traceability and authenticity of tea products and form the basis for the development of strategies against fraudulent practices.
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Affiliation(s)
- Georgios Lagiotis
- The Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Evangelia Stavridou
- The Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Irini Bosmali
- The Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Maslin Osathanunkul
- The Department of Biology, Faculty of Science and also from Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nadia Haider
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission (AEC), Damascus, Syria
| | - Panagiotis Madesis
- The Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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Whitehurst LE, Cunard CE, Reed JN, Worthy SJ, Marsico TD, Lucardi RD, Burgess KS. Preliminary application of DNA barcoding toward the detection of viable plant propagules at an initial, international point-of-entry in Georgia, USA. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02204-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Urumarudappa SKJ, Tungphatthong C, Sukrong S. Mitigating the Impact of Admixtures in Thai Herbal Products. Front Pharmacol 2019; 10:1205. [PMID: 31749698 PMCID: PMC6843083 DOI: 10.3389/fphar.2019.01205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/17/2019] [Indexed: 12/29/2022] Open
Abstract
Medicinal plants and their products are extensively used within indigenous healthcare systems in Thailand and several other nations. The international trade of herbal products has a noteworthy impact on the worldwide economy, and the interest in herbal products is expanding in both developing and developed countries. There has been rapid growth in the medicinal plant product market and a broadening consumer base interested in herbal products from Thailand. However, in herbal industries, ingredient substitution and admixture are typical issues wherein species of lower market value are admixed with those of a higher value. The adverse consequences of consuming adulterated drugs are invariably due to the presence of an unintended herb rather than the presence of an intended herb. It has also been argued that admixtures are intentional because of the lack of regulatory policies or centralized tests for product authentication. The consequences of species admixtures can extend from the reduced efficacy of a drug to decreased trade value. This study aims to clarify the nature and extent of species admixtures reported in the Thai herbal trade market and discuss the potential reasons for such adulteration. In the broader context of species admixtures, we strongly propose the establishment of multiple herbal crude drug repositories that can be developed to facilitate the use of comparative identity tests by industry, traders, and researchers to maintain authentic natural health product (NHP) standards and to certify the authenticity of NHPs. The proposition of the establishment of centralized testing (CT) could be a promising initiative in Thailand for the development of science and technology, and the herbal medicines produced as a result of CT could be dispensed as prescription drugs based on disease consideration instead of as health foods or nutraceuticals.
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Affiliation(s)
- Santhosh Kumar J Urumarudappa
- Research Unit of DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Chayapol Tungphatthong
- Research Unit of DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Suchada Sukrong
- Research Unit of DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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15
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Alfeche NKG, Binag SDA, Medecilo MMP, Alejandro GJD. Standard reference material (SRM) DNA barcode library approach for authenticating Antidesma bunius (L.) Spreng. (bignay) derived herbal medicinal products. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:1777-1786. [PMID: 31596175 DOI: 10.1080/19440049.2019.1670868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the Philippines, the herbal medicinal product (HMP) market is flourishing due to the abundance of pharmacologically important species, and the high level of ethnomedicinal knowledge still widely accepted by the public. As such, herbal products from Antidesma bunius (L.) Spreng., locally known as bignay, are popular as medicine for various ailments of the circulatory and digestive systems. Though efficacy is guaranteed, the authenticity of the marketed products is still in question as several other herbal plants can provide the said benefits. Similar morphology between wild species also hinders species identification and contributes confusion especially to the general consumer. The authenticity of the marketed HMPs was established by means of DNA barcoding techniques which offers quick and reliable species identification by means of (1) the Basic Local Alignment Search Tool (BLASTn) and (2) the establishment of the first Standard Reference Material (SRM) Herbal barcode library for Antidesma spp. A total of 56 gene accessions from matK-psbA-trnH-rbcL sequences of 9 wild Antidesma spp. comprised the SRM which was then used to confirm the identity of 11 randomly sampled bignay-derived HMPs. Following the BLASTn and the SRM (maximum likelihood tree reconstruction) criterion, the subjected sequences revealed that only three of the 11 HMPs were authentic A. bunius-derived products. The other eight HMPs contained substitutes that were either fillers or different herbal medicinal plant not indicated in the product labels. These results indicate that product safety should be reinforced with complete HMP authentication using traditional methods supported by molecular data.
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Affiliation(s)
- Niña Kathryn G Alfeche
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines.,Plant Sciences Laboratory, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Center, University of Santo Tomas, Manila, Philippines
| | - Sam Dominic A Binag
- Plant Sciences Laboratory, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Center, University of Santo Tomas, Manila, Philippines
| | - Maria Melanie P Medecilo
- Biological Sciences Department and University Research Office, De La Salle University - Dasmarinas, Cavite, Philippines
| | - Grecebio Jonathan D Alejandro
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines.,Plant Sciences Laboratory, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Center, University of Santo Tomas, Manila, Philippines
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16
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Amane D, Ananthanarayan L. Detection of adulteration in black gram-based food products using DNA barcoding. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.04.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Yang ML, Rice E, Leimbach-Maus H, Partridge CG. Identification and characterization of Gypsophila paniculata color morphs in Sleeping Bear Dunes National Lakeshore, MI, USA. PeerJ 2019; 7:e7100. [PMID: 31245177 PMCID: PMC6585908 DOI: 10.7717/peerj.7100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/08/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Gypsophila paniculata (baby's breath) is an invasive species found throughout much of the northwest United States and western Canada. Recently, plants exhibiting a different color morphology were identified within the coastal dunes along eastern Lake Michigan. The common baby's breath (G. paniculata) typically produces stems that are purple in color (purple morph), while the atypical morph has stems that are green-yellow (green-yellow morph). The purpose of this study was to characterize these newly identified morphs and determine if they are genetically distinct species from the common baby's breath in order to assess whether alternative management strategies should be employed to control these populations. METHODS We sequenced two chloroplast regions, ribulose-bisphosphate carboxylase gene (rbcL), and maturase K (matK), and one nuclear region, internal transcribed spacer 2 (ITS2), from the purple morphs and green-yellow morphs collected from Sleeping Bear Dunes National Lakeshore, MI, USA (SBDNL). Sequences were aligned to reference sequences from other Gypsophila species obtained from the Barcode of Life Database and GenBank databases. We also collected seeds from wild purple morph and wild green-yellow morph plants in SBDNL. We grew the seeds in a common garden setting and characterized the proportion of green-yellow individuals produced from the two color morphs after 5-months of growth. RESULTS Phylogenetic analyses based upon rbcL, matK, and ITS2 regions suggest that the two color morphs are not distinct species and they both belong to G. paniculata. Seeds collected from wild green-yellow morphs produced a significantly higher proportion of green-yellow individuals compared to the number produced by seeds collected from wild purple morphs. However, seeds collected from both color morphs produced more purple morphs than green-yellow morphs. DISCUSSION Based upon these results, we propose that the two color morphs are variants of G. paniculata. Given the significant difference in the number of green-yellow morphs produced from the seeds of each morph type, we also suggest that this color difference has some genetic basis. We propose that current management continue to treat the two color morphs in a similar manner in terms of removal to prevent the further spread of this species.
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Affiliation(s)
- Marisa L. Yang
- Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Emma Rice
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Hailee Leimbach-Maus
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Charlyn G. Partridge
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
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18
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Basak S, Aadi Moolam R, Parida A, Mitra S, Rangan L. Evaluation of rapid molecular diagnostics for differentiating medicinal Kaempferia species from its adulterants. PLANT DIVERSITY 2019; 41:206-211. [PMID: 31453420 PMCID: PMC6704042 DOI: 10.1016/j.pld.2019.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 06/10/2023]
Abstract
Accurate detection of unique herbs is crucial for herbal medicine preparation. Zingiberaceae species, which are important in Ayurvedic medicine of India, are often misidentified in Northeast (NE) Indian herbal markets. Kaempferia galanga (Zingiberaceae) is one of the major components of popular Ayurvedic drugs used for rheumatic diseases (i.e., "Gandha Thailam" and "Rasnairandadi Kashayam"), contusions, fractures, and sprains. In NE India, herbal healers often misidentify plants from the Marantaceae family (e.g., Calathea bachemiana and Maranta leuconeura) as Kaempferia, which leads to adulteration of the medicinal herb. This misidentification of herbs occurs in NE India because Zingiberaceae plant barcoding information is inadequate. As a consequence, herbal medicine is not only therapeutically less effective but may also cause adverse reactions that range from mild to life-threatening. In this study, we used eight barcoding loci to develop "fingerprints" for four Kaempferia species and two species frequently mistaken for Kaempferia. The PCR and sequencing success of the loci matK, rbcL and trnH-psbA were found to be 100%; the combination of matK, rbcL, and trnH-psbA proved to be the ideal locus for discriminating the Kaempferia species from their adulterants because the combined loci showed greater variability than individual loci. This reliable tool was therefore developed in the current study for accurate identification of Kaempferia plants which can effectively resolve identification issues for herbal healers.
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Affiliation(s)
- Supriyo Basak
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781 039, India
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ramesh Aadi Moolam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781 039, India
| | - Ajay Parida
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India
| | - Sudip Mitra
- Centre for Rural Technology, Indian Institute of Technology Guwahati, Assam, 781 039, India
| | - Latha Rangan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781 039, India
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19
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Zhang P, Liu C, Zheng X, Wu L, Liu Z, Liao B, Shi Y, Li X, Xu J, Chen S. Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures. Genes (Basel) 2019; 10:E343. [PMID: 31067783 PMCID: PMC6562688 DOI: 10.3390/genes10050343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/22/2019] [Accepted: 04/29/2019] [Indexed: 11/22/2022] Open
Abstract
DNA barcoding has been used for decades, although it has mostly been applied to somesingle-species. Traditional Chinese medicine (TCM), which is mainly used in the form ofcombination-one type of the multi-species, identification is crucial for clinical usage.Next-generation Sequencing (NGS) has been used to address this authentication issue for the pastfew years, but conventional NGS technology is hampered in application due to its short sequencingreads and systematic errors. Here, a novel method, Full-length multi-barcoding (FLMB) vialong-read sequencing, is employed for the identification of biological compositions in herbalcompound formulas in adequate and well controlled studies. By directly sequencing the full-lengthamplicons of ITS2 and psbA-trnH through single-molecule real-time (SMRT) technology, thebiological composition of a classical prescription Sheng-Mai-San (SMS) was analyzed. At the sametime, clone-dependent Sanger sequencing was carried out as a parallel control. Further, anotherformula-Sanwei-Jili-San (SJS)-was analyzed with genes of ITS2 and CO1. All the ingredients inthe samples of SMS and SJS were successfully authenticated at the species level, and 11 exogenousspecies were also checked, some of which were considered as common contaminations in theseproducts. Methodology analysis demonstrated that this method was sensitive, accurate andreliable. FLMB, a superior but feasible approach for the identification of biological complexmixture, was established and elucidated, which shows perfect interpretation for DNA barcodingthat could lead its application in multi-species mixtures.
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Affiliation(s)
- Peng Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Chunsheng Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Xiasheng Zheng
- Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhixiang Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Baosheng Liao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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20
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Omelchenko DO, Speranskaya AS, Ayginin AA, Khafizov K, Krinitsina AA, Fedotova AV, Pozdyshev DV, Shtratnikova VY, Kupriyanova EV, Shipulin GA, Logacheva MD. Improved Protocols of ITS1-Based Metabarcoding and Their Application in the Analysis of Plant-Containing Products. Genes (Basel) 2019; 10:genes10020122. [PMID: 30736447 PMCID: PMC6409534 DOI: 10.3390/genes10020122] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Plants are widely used for food and beverage preparation, most often in the form of complex mixtures of dried and ground parts, such as teas, spices or herbal medicines. Quality control of such products is important due to the potential health risks from the presence of unlabelled components or absence of claimed ones. A promising approach to analyse such products is DNA metabarcoding due to its high resolution and sensitivity. However, this method’s application in food analysis requires several methodology optimizations in DNA extraction, amplification and library preparation. In this study, we present such optimizations. The most important methodological outcomes are the following: (1) the DNA extraction method greatly influences amplification success; (2) the main problem for the application of metabarcoding is DNA purity, not integrity or quantity; and (3) the “non-amplifiable” samples can be amplified with polymerases resistant to inhibitors. Using this optimized workflow, we analysed a broad set of plant products (teas, spices and herbal remedies) using two NGS platforms. The analysis revealed the problem of both the presence of extraneous components and the absence of labelled ones. Notably, for teas, no correlation was found between the price and either the absence of labelled components or presence of unlabelled ones; for spices, a negative correlation was found between the price and presence of unlabelled components.
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Affiliation(s)
- Denis O Omelchenko
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Institute for Information Transmission Problems, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
| | - Anna S Speranskaya
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Central Research Institute of Epidemiology, Novogireevskaya St. 3а, Moscow 111123, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Andrey A Ayginin
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Moscow Institute of Physics and Technology, Institutskiy Ln. 9, Dolgoprudny 141701, Moscow Region, Russia.
| | - Kamil Khafizov
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Central Research Institute of Epidemiology, Novogireevskaya St. 3а, Moscow 111123, Russia.
- Moscow Institute of Physics and Technology, Institutskiy Ln. 9, Dolgoprudny 141701, Moscow Region, Russia.
- Center for Strategic Planning, Ministry of Health of the Russian Federation, Pogodinskaya St. 10, build.1, Moscow 119121, Russia.
| | - Anastasia A Krinitsina
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Anna V Fedotova
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Denis V Pozdyshev
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Viktoria Y Shtratnikova
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Evgenia V Kupriyanova
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - German A Shipulin
- Center for Strategic Planning, Ministry of Health of the Russian Federation, Pogodinskaya St. 10, build.1, Moscow 119121, Russia.
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Institute for Information Transmission Problems, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
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Amandita FY, Rembold K, Vornam B, Rahayu S, Siregar IZ, Kreft H, Finkeldey R. DNA barcoding of flowering plants in Sumatra, Indonesia. Ecol Evol 2019; 9:1858-1868. [PMID: 30847077 PMCID: PMC6392390 DOI: 10.1002/ece3.4875] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/02/2022] Open
Abstract
The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land-use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best-close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best-close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two-loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty-one species were found to be nonmonophyletic with both markers. The two-loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.
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Affiliation(s)
- Fitri Y. Amandita
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
- Research and Development Center for Environmental Quality and Laboratory
| | - Katja Rembold
- Biodiversity, Macroecology, and Biogeography Research GroupGeorg‐August UniversityGöttingenGermany
- Botanical Garden of the University of BernBernSwitzerland
| | - Barbara Vornam
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
| | - Sri Rahayu
- Bogor Botanical GardenLembaga Ilmu Pengetahuan IndonesiaBogorIndonesia
| | | | - Holger Kreft
- Biodiversity, Macroecology, and Biogeography Research GroupGeorg‐August UniversityGöttingenGermany
| | - Reiner Finkeldey
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August UniversityGöttingenGermany
- University of KasselKasselGermany
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Tnah L, Lee S, Tan A, Lee C, Ng K, Ng C, Nurul Farhanah Z. DNA barcode database of common herbal plants in the tropics: a resource for herbal product authentication. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Speranskaya AS, Krinitsina AA, Shipulin GA, Khafizov KF, Logacheva MD. High-Throughput Sequencing for the Authentication of Food Products: Problems and Perspectives. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Waldo JT, Pereira M, Rahman M, Siconolfi J. Development and validation of an undergraduate laboratory activity exploring the dna analysis of pet food. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:536-546. [PMID: 30369033 DOI: 10.1002/bmb.21165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
A novel experiment has been developed with a goal of enhancing engagement and deepening understanding of fundamental molecular biology concepts. In this laboratory activity, students investigate the composition of pet foods through quantitative polymerase chain reaction (qPCR) analysis. By conducting this experiment, students address a scientific question that has the potential to be of personal interest and they gain an appreciation of the power of genetic analysis. To develop this activity, ingredient lists of popular pet foods were surveyed and eight different components were selected to be the subject of inquiry. Reaction conditions for qPCR were validated and optimized, and a simple, efficient, and student-friendly protocol was developed. A cohort of upper-level biology students extracted DNA from pet foods and conducted the qPCR reactions. Specificity of amplification was determined by conducting melting point analysis and agarose gel electrophoresis of the products. Student reactions were analyzed and efficacy of this approach for deepening understanding of fundamental biochemical and molecular biology concepts was documented. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):536-546, 2018.
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Affiliation(s)
- Jennifer Turner Waldo
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
| | - Melanie Pereira
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
| | - Mohammad Rahman
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
| | - Jessica Siconolfi
- Department of Biology, State University of New York at New Paltz, New Paltz, New York
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25
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Marizzi C, Florio A, Lee M, Khalfan M, Ghiban C, Nash B, Dorey J, McKenzie S, Mazza C, Cellini F, Baria C, Bepat R, Cosentino L, Dvorak A, Gacevic A, Guzman-Moumtzis C, Heller F, Holt NA, Horenstein J, Joralemon V, Kaur M, Kaur T, Khan A, Kuppan J, Laverty S, Lock C, Pena M, Petrychyn I, Puthenkalam I, Ram D, Ramos A, Scoca N, Sin R, Gonzalez I, Thakur A, Usmanov H, Han K, Wu A, Zhu T, Micklos DA. DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists. PLoS One 2018; 13:e0199015. [PMID: 30020927 PMCID: PMC6051577 DOI: 10.1371/journal.pone.0199015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/30/2018] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.
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Affiliation(s)
- Christine Marizzi
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Antonia Florio
- Department of Herpetology, American Museum of Natural History, New York, New York, United States of America
| | - Melissa Lee
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Mohammed Khalfan
- New York University, New York, New York, United States of America
| | - Cornel Ghiban
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Bruce Nash
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jenna Dorey
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- The New York Botanical Garden, Bronx, New York, United States of America
| | - Sean McKenzie
- The Rockefeller University, New York, New York, United States of America
| | - Christine Mazza
- Genovesi Environmental Study Center, New York City Department of Education, Brooklyn, New York, United States of America
| | - Fabiana Cellini
- Genovesi Environmental Study Center, New York City Department of Education, Brooklyn, New York, United States of America
| | - Carlo Baria
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Ron Bepat
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Lena Cosentino
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Alexander Dvorak
- International High School at Union Square, New York City Department of Education New York, New York, United States of America
| | - Amina Gacevic
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Cristina Guzman-Moumtzis
- Frank McCourt High School, New York City Department of Education, New York, New York, United States of America
| | - Francesca Heller
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Nicholas Alexander Holt
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Jeffrey Horenstein
- Stuyvesant High School, New York City Department of Education, New York, New York, United States of America
| | - Vincent Joralemon
- Frank McCourt High School, New York City Department of Education, New York, New York, United States of America
| | - Manveer Kaur
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Tanveer Kaur
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Armani Khan
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Jessica Kuppan
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Scott Laverty
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Camila Lock
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Marianne Pena
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Ilona Petrychyn
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Indu Puthenkalam
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Daval Ram
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Arlene Ramos
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Noelle Scoca
- Brooklyn International High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Rachel Sin
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Izabel Gonzalez
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Akansha Thakur
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Husan Usmanov
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Karen Han
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Andy Wu
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Tiger Zhu
- Stuyvesant High School, New York City Department of Education, New York, New York, United States of America
| | - David Andrew Micklos
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
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Magona N, Richardson DM, Le Roux JJ, Kritzinger-Klopper S, Wilson JRU. Even well-studied groups of alien species might be poorly inventoried: Australian Acacia species in South Africa as a case study. NEOBIOTA 2018. [DOI: 10.3897/neobiota.39.23135] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Understanding the status and extent of spread of alien plants is crucial for effective management. We explore this issue using Australian Acacia species (wattles) in South Africa (a global hotspot for wattle introductions and tree invasions). The last detailed inventory of wattles in South Africa was based on data collated forty years ago. This paper aimed to determine: 1) how many Australian Acacia species have been introduced to South Africa; 2) which species are still present; and 3) the status of naturalised taxa that might be viable targets for eradication. All herbaria in South Africa with specimens of introduced Australian Acacia species were visited and locality records were compared with records from literature sources, various databases, and expert knowledge. For taxa not already known to be widespread invaders, field surveys were conducted to determine whether plants are still present, and detailed surveys were undertaken of all naturalised populations. To confirm the putative identities of the naturalised taxa, we also sequenced one nuclear and one chloroplast gene. We found evidence that 141 Australian Acacia species have been introduced to South Africa (approximately double the estimate from previous work), but we could only confirm the current presence of 33 species. Fifteen wattle species are invasive (13 are in category E and two in category D2 in the Unified Framework for Biological Invasions); five have naturalised (C3); and 13 are present but there was no evidence that they had produced reproductive offspring (B2 or C1). DNA barcoding provided strong support for only 23 taxa (including two species not previously recorded from South Africa), the current name ascribed was not supported for three species and, for a further three species, there was no voucher specimen on GenBank against which their identity could be checked. Given the omissions and errors found during this systematic re-evaluation of historical records, it is clear that analyses of the type conducted here are crucial if the status of even well-studied groups of alien taxa is to be accurately determined.
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Next generation crop improvement program: Progress and prospect in tea ( Camellia sinensis (L.) O. Kuntze). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aasci.2018.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Raclariu AC, Heinrich M, Ichim MC, de Boer H. Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:123-128. [PMID: 28906059 PMCID: PMC5836936 DOI: 10.1002/pca.2732] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/23/2017] [Accepted: 08/26/2017] [Indexed: 05/21/2023]
Abstract
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.
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Affiliation(s)
- Ancuta Cristina Raclariu
- Natural History MuseumUniversity of OsloP.O. Box 1172, Blindern0318OsloNorway
- Stejarul Research Centre for Biological SciencesNational Institute of Research and Development for Biological SciencesAlexandru cel Bun Street, 6610004Piatra NeamtRomania
| | - Michael Heinrich
- Research Group of Pharmacognosy and Phytotherapy, Research Cluster ‘Biodiversity and Medicines’, UCL School of PharmacyUniversity of London29–39 Brunswick SqLondonWC1N 1AXUK
| | - Mihael Cristin Ichim
- Stejarul Research Centre for Biological SciencesNational Institute of Research and Development for Biological SciencesAlexandru cel Bun Street, 6610004Piatra NeamtRomania
| | - Hugo de Boer
- Natural History MuseumUniversity of OsloP.O. Box 1172, Blindern0318OsloNorway
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A protocol for obtaining DNA barcodes from plant and insect fragments isolated from forensic-type soils. Int J Legal Med 2018; 132:1515-1526. [PMID: 29423711 DOI: 10.1007/s00414-018-1772-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
Soil is often collected from a suspect's tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]. A DNA barcode protocol suitable for processing forensic-type biological fragments was developed and its utility broadly tested with forensic-type fragments (e.g., seeds, leaves, bark, head, legs; n, 213) isolated from soils collected within Virginia, USA (n, 11). Difficulties with PCR inhibitors in plant extracts and obtaining clean Sanger sequence data from insect amplicons were encountered during protocol development; however, the final protocol produced sequences specific to the expected locus and taxa. The overall quantity and quality of DNA extracted from the 213 forensic-type biological fragments was low (< 15 ng/μL). For plant fragments, only the rbcL sequence data was deemed reliable; thus, taxonomic identifications were limited to the family level. The majority of insect sequences matched COI in both GenBank and Barcode of Life DataSystems; however, they were identified as an undescribed environmental contaminant. Although limited taxonomic information was gleaned from the forensic-type fragments processed in this study, the new protocol shows promise for obtaining reliable and specific identifications through DNA barcoding, which could ultimately enhance the information gleaned from soil examinations.
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Liu J, Shi L, Song J, Sun W, Han J, Liu X, Hou D, Yao H, Li M, Chen S. BOKP: A DNA Barcode Reference Library for Monitoring Herbal Drugs in the Korean Pharmacopeia. Front Pharmacol 2017; 8:931. [PMID: 29326593 PMCID: PMC5742532 DOI: 10.3389/fphar.2017.00931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 12/11/2017] [Indexed: 11/13/2022] Open
Abstract
Herbal drug authentication is an important task in traditional medicine; however, it is challenged by the limitations of traditional authentication methods and the lack of trained experts. DNA barcoding is conspicuous in almost all areas of the biological sciences and has already been added to the British pharmacopeia and Chinese pharmacopeia for routine herbal drug authentication. However, DNA barcoding for the Korean pharmacopeia still requires significant improvements. Here, we present a DNA barcode reference library for herbal drugs in the Korean pharmacopeia and developed a species identification engine named KP-IDE to facilitate the adoption of this DNA reference library for the herbal drug authentication. Using taxonomy records, specimen records, sequence records, and reference records, KP-IDE can identify an unknown specimen. Currently, there are 6,777 taxonomy records, 1,054 specimen records, 30,744 sequence records (ITS2 and psbA-trnH) and 285 reference records. Moreover, 27 herbal drug materials were collected from the Seoul Yangnyeongsi herbal medicine market to give an example for real herbal drugs authentications. Our study demonstrates the prospects of the DNA barcode reference library for the Korean pharmacopeia and provides future directions for the use of DNA barcoding for authenticating herbal drugs listed in other modern pharmacopeias.
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Affiliation(s)
- Jinxin Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical College, Chengde, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xia Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dianyun Hou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingyue Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shilin Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Osathanunkul M, Dheeranupattana S, Rotarayanont S, Sookkhee S, Osathanunkul K, Madesis P. Evaluation of suitable DNA regions for molecular identification of high value medicinal plants in genus Kaempferia. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:726-735. [PMID: 29215948 DOI: 10.1080/15257770.2017.1391393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Kaempferia (Zingiberaceae). Four primer pairs were evaluated (rbcL, rpoC, trnL and ITS1). It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Thus, the primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL primer pair gave the lowest resolution. Our Bar-HRM developed here would not only be useful for identification of Kaempferia plant specimens lacking essential parts for morphological identification but will be useful for authenticating products in powdered form of a high value medicinal species Kaempferia parviflora, in particular.
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Affiliation(s)
- Maslin Osathanunkul
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai , Thailand.,b Center of Excellence in Bioresources for Agriculture, Industry and Medicine , Chiang Mai University , Chiang Mai , Thailand
| | | | - Siriphron Rotarayanont
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai , Thailand
| | - Siriwoot Sookkhee
- c Department of Microbiology, Faculty of Medicine , Chiang Mai University , Chiang Mai , Thailand
| | - Khukrit Osathanunkul
- d Department of Information Technology , International College, Payap University , Chiang Mai , Thailand
| | - Panagiotis Madesis
- e Institute of Applied Biosciences , Centre for Research & Technology Hellas (CERTH) , Thessaloniki , Greece
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Osathanunkul M, Ounjai S, Osathanunkul R, Madesis P. Evaluation of a DNA-based method for spice/herb authentication, so you do not have to worry about what is in your curry, buon appetito! PLoS One 2017; 12:e0186283. [PMID: 29020084 PMCID: PMC5636142 DOI: 10.1371/journal.pone.0186283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/28/2017] [Indexed: 12/27/2022] Open
Abstract
It is long believed that some spices may help protect against certain chronic conditions. Spices are usually parts of plants that have been powdered into small pieces. Have you ever wondered what the curry powder in your dish is made of? The aim of this work was to develop an appropriate DNA-based method for assessment of spice identity. Selecting the best marker for species recognition in the Zingiberaceae family. Six DNA regions were investigated in silico, including ITS, matK, rbcL, rpoC, trnH-psbA and trnL. Then, only four regions (ITS, matK, rbcL and trnH-psbA) were included in the simulated HRM (High-resolution Melting) analysis as the results from previous analysis showed that rpoC and trnL may not be suitable to be used to identify Zingiberaceae species in HRM analysis based on both the percentage of nucleotide variation and GC content. Simulated HRM analysis was performed to test the feasibility of Bar-HRM. We found that ITS2 is the most effective region to be used for identification of the studied species and thus was used in laboratory HRM analysis. All seven tested Zingiberaceae plants were then able to be distinguished using the ITS2 primers in laboratory HRM. Most importantly the melting curves gained from fresh and dried tissue overlapped, which is a crucial outcome for the applicability of the analysis. The method could be used in an authentication test for dried products. In the authentication test, only one of seven store-sold Zingiberaceae products that were tested contained the species listed on their labels, while we found substitution/contamination of the tested purchased products in the rest.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| | - Sarawut Ounjai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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Li L, Josef BA, Liu B, Zheng S, Huang L, Chen S. Three-Dimensional Evaluation on Ecotypic Diversity of Traditional Chinese Medicine: A Case Study of Artemisia annua L. FRONTIERS IN PLANT SCIENCE 2017; 8:1225. [PMID: 28744301 PMCID: PMC5504922 DOI: 10.3389/fpls.2017.01225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/28/2017] [Indexed: 05/04/2023]
Abstract
Artemisinin is the first-line drug for anti-malaria recommended by the World Health Organization (WHO). As the sole natural plant source of artemisinin, ecotypes of Artemisia annua L. vary widely in artemisinin content between nations, and China is the main producing area of A. annua. Here we present a three-dimensional evaluation on ecotypic diversity of A. annua from 12 main producing areas in China using high-performance liquid chromatography coupled with evaporative light scattering detection (HPLC-ELSD) method, DNA barcoding and ecological analyses. The results indicated that A. annua exhibited high ecotypic diversity. A. annua grown in the South of the Qinling Mountains-Huaihe River Line had a high artemisinin content, whereas the northern ones were low. Similar pattern was noted in the genetic diversity. The southern A. annua had high intraspecific variation in contrast to the northern A. annua. In terms of ecological analyses, humidity and sunshine time could be the major limiting ecological factors that affect the accumulation of artemisinin. This is the first reported three-dimensional evaluation integrating chemical, molecular and ecological analyses of the ecotypic diversity of A. annua. The work will facilitate exploring the genetic basis of chemical variations and developing strategies for the breeding and cultivation of high quality A. annua.
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Affiliation(s)
- Lin Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Brinckmann A. Josef
- Sustainability Department, Traditional Medicinals, SebastopolCA, United States
| | - Bing Liu
- Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Sihao Zheng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Linfang Huang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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Dhar B, Ghosh SK. Mini-DNA barcode in identification of the ornamental fish: A case study from Northeast India. Gene 2017; 627:248-254. [PMID: 28652184 DOI: 10.1016/j.gene.2017.06.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 05/28/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022]
Abstract
The ornamental fishes were exported under the trade names or generic names, thus creating problems in species identification. In this regard, DNA barcoding could effectively elucidate the actual species status. However, the problem arises if the specimen is having taxonomic disputes, falsified by trade/generic names, etc., On the other hand, barcoding the archival museum specimens would be of greater benefit to address such issues as it would create firm, error-free reference database for rapid identification of any species. This can be achieved only by generating short sequences as DNA from chemically preserved are mostly degraded. Here we aimed to identify a short stretch of informative sites within the full-length barcode segment, capable of delineating diverse group of ornamental fish species, commonly traded from NE India. We analyzed 287 full-length barcode sequences from the major fish orders and compared the interspecific K2P distance with nucleotide substitutions patterns and found a strong correlation of interspecies distance with transversions (0.95, p<0.001). We, therefore, proposed a short stretch of 171bp (transversion rich) segment as mini-barcode. The proposed segment was compared with the full-length barcodes and found to delineate the species effectively. Successful PCR amplification and sequencing of the 171bp segment using designed primers for different orders validated it as mini-barcodes for ornamental fishes. Thus, our findings would be helpful in strengthening the global database with the sequence of archived fish species as well as an effective identification tool of the traded ornamental fish species, as a less time consuming, cost effective field-based application.
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Affiliation(s)
- Bishal Dhar
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India; University of Kalyani, Kalyani 741235, West Bengal, India.
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Raclariu AC, Mocan A, Popa MO, Vlase L, Ichim MC, Crisan G, Brysting AK, de Boer H. Veronica officinalis Product Authentication Using DNA Metabarcoding and HPLC-MS Reveals Widespread Adulteration with Veronica chamaedrys. Front Pharmacol 2017; 8:378. [PMID: 28674497 PMCID: PMC5474480 DOI: 10.3389/fphar.2017.00378] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
Studying herbal products derived from local and traditional knowledge and their value chains is one of the main challenges in ethnopharmacology. The majority of these products have a long history of use, but non-harmonized trade and differences in regulatory policies between countries impact their value chains and lead to concerns over product efficacy, safety and quality. Veronica officinalis L. (common speedwell), a member of Plantaginaceae family, has a long history of use in European traditional medicine, mainly in central eastern Europe and the Balkans. However, no specified control tests are available either to establish the quality of derived herbal products or for the discrimination of its most common substitute, V. chamaedrys L. (germander speedwell). In this study, we use DNA metabarcoding and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS) to authenticate sixteen V. officinalis herbal products and compare the potential of the two approaches to detect substitution, adulteration and the use of unreported constituents. HPLC-MS showed high resolution in detecting phytochemical target compounds, but did not enable detection of specific plant species in the products. DNA metabarcoding detected V. officinalis in only 15% of the products, whereas it detected V. chamaedrys in 62% of the products. The results confirm that DNA metabarcoding can be used to test for the presence of Veronica species, and detect substitution and/or admixture of other Veronica species, as well as simultaneously detect all other species present. Our results confirm that none of the herbal products contained exactly the species listed on the label, and all included substitutes, contaminants or fillers. This study highlights the need for authentication of raw herbals along the value chain of these products. An integrative methodology can assess both the quality of herbal products in terms of target compound concentrations and species composition, as well as admixture and substitution with other chemical compounds and plants.
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Affiliation(s)
- Ancuta C Raclariu
- Plant Evolution and Metabarcoding Group, Natural History Museum, University of OsloOslo, Norway.,Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Andrei Mocan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania.,ICHAT and Institute for Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaCluj-Napoca, Romania
| | - Madalina O Popa
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Laurian Vlase
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of OsloOslo, Norway
| | - Mihael C Ichim
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Gianina Crisan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania
| | - Anne K Brysting
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)Oslo, Norway
| | - Hugo de Boer
- Plant Evolution and Metabarcoding Group, Natural History Museum, University of OsloOslo, Norway.,Department of Organismal Biology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
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De Castro O, Comparone M, Di Maio A, Del Guacchio E, Menale B, Troisi J, Aliberti F, Trifuoggi M, Guida M. What is in your cup of tea? DNA Verity Test to characterize black and green commercial teas. PLoS One 2017; 12:e0178262. [PMID: 28542606 PMCID: PMC5441638 DOI: 10.1371/journal.pone.0178262] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/04/2017] [Indexed: 01/10/2023] Open
Abstract
In this study, we used several molecular techniques to develop a fast and reliable protocol (DNA Verity Test, DVT) for the characterization and confirmation of the species or taxa present in herbal infusions. As a model plant for this protocol, Camellia sinensis, a traditional tea plant, was selected due to the following reasons: its historical popularity as a (healthy) beverage, its high selling value, the importation of barely recognizable raw product (i.e., crushed), and the scarcity of studies concerning adulterants or contamination. The DNA Verity Test includes both the sequencing of DNA barcoding markers and genotyping of labeled-PCR DNA barcoding fragments for each sample analyzed. This protocol (DVT) was successively applied to verify the authenticity of 32 commercial teas (simple or admixture), and the main results can be summarized as follows: (1) the DVT protocol is suitable to detect adulteration in tea matrices (contaminations or absence of certified ingredients), and the method can be exported for the study of other similar systems; (2) based on the BLAST analysis of the sequences of rbcL+matK±rps7-trnV(GAC) chloroplast markers, C. sinensis can be taxonomically characterized; (3) rps7-trnV(GAC) can be employed to discriminate C. sinensis from C. pubicosta; (4) ITS2 is not an ideal DNA barcode for tea samples, reflecting potential incomplete lineage sorting and hybridization/introgression phenomena in C. sinensis taxa; (5) the genotyping approach is an easy, inexpensive and rapid pre-screening method to detect anomalies in the tea templates using the trnH(GUG)-psbA barcoding marker; (6) two herbal companies provided no authentic products with a contaminant or without some of the listed ingredients; and (7) the leaf matrices present in some teabags could be constituted using an admixture of different C. sinensis haplotypes and/or allied species (C. pubicosta).
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Affiliation(s)
- Olga De Castro
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | - Maria Comparone
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | - Antonietta Di Maio
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | | | - Bruno Menale
- Department of Biology, Botanical Garden, University of Naples Federico II, Naples Italy
| | - Jacopo Troisi
- Department of Medicine and Surgery and Dentistry, University of Salerno, Salerno, Italy
| | | | - Marco Trifuoggi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Naples Italy
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Raclariu AC, Paltinean R, Vlase L, Labarre A, Manzanilla V, Ichim MC, Crisan G, Brysting AK, de Boer H. Comparative authentication of Hypericum perforatum herbal products using DNA metabarcoding, TLC and HPLC-MS. Sci Rep 2017; 7:1291. [PMID: 28465563 PMCID: PMC5431008 DOI: 10.1038/s41598-017-01389-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/29/2017] [Indexed: 12/03/2022] Open
Abstract
Many herbal products have a long history of use, but there are increasing concerns over product efficacy, safety and quality in the wake of recent cases exposing discrepancies between labeling and constituents. When it comes to St. John’s wort (Hypericum perforatum L.) herbal products, there is limited oversight, frequent off-label use and insufficient monitoring of adverse drug reactions. In this study, we use amplicon metabarcoding (AMB) to authenticate 78 H. perforatum herbal products and evaluate its ability to detect substitution compared to standard methods using thin-layer chromatography (TLC) and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS). Hypericum perforatum was detected in 68% of the products using AMB. Furthermore, AMB detected incongruence between constituent species and those listed on the label in all products. Neither TLC nor HPLC-MS could be used to unambiguously identify H. perforatum. They are accurate methods for authenticating presence of the target compounds, but have limited efficiency in detecting infrageneric substitution and do not yield any information on other plant ingredients in the products. Random post-marketing AMB of herbal products by regulatory agencies could raise awareness among consumers of substitution and would provide an incentive to manufacturers to increase quality control from raw ingredients to commercialized products.
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Affiliation(s)
- Ancuta Cristina Raclariu
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.,NIRDBS/"Stejarul" Research Centre for Biological Sciences, Alexandru cel Bun Street, 6, 610004, Piatra, Neamt, Romania
| | - Ramona Paltinean
- Department of Pharmaceutical Botany, University of Medicine and Pharmacy "Iuliu Haţieganu", Faculty of Pharmacy, Gheorghe Marinescu Street, 23, 400337, Cluj-Napoca, Romania
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmaceutics, "Iuliu Hatieganu" University of Medicine and Pharmacy, Ion Creanga Street, 8-10, 400010, Cluj-Napoca, Romania
| | - Aurélie Labarre
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Vincent Manzanilla
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Mihael Cristin Ichim
- NIRDBS/"Stejarul" Research Centre for Biological Sciences, Alexandru cel Bun Street, 6, 610004, Piatra, Neamt, Romania
| | - Gianina Crisan
- Department of Pharmaceutical Botany, University of Medicine and Pharmacy "Iuliu Haţieganu", Faculty of Pharmacy, Gheorghe Marinescu Street, 23, 400337, Cluj-Napoca, Romania
| | - Anne Krag Brysting
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | - Hugo de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.
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Mohammed Abubakar B, Mohd Salleh F, Shamsir Omar MS, Wagiran A. Review: DNA Barcoding and Chromatography Fingerprints for the Authentication of Botanicals in Herbal Medicinal Products. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2017; 2017:1352948. [PMID: 28536641 PMCID: PMC5425840 DOI: 10.1155/2017/1352948] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/11/2017] [Accepted: 03/16/2017] [Indexed: 01/28/2023]
Abstract
In the last two decades, there has been a tremendous increase in the global use of herbal medicinal products (HMPs) due to their claimed health benefits. This has led to increase in their demand and consequently, also, resulted in massive adulteration. This is due to the fact that most of the traditional methods cannot identify closely related species in a process product form. Therefore the urgent need for simple and rapid identification methods resulted in the discovery of a novel technique. DNA barcoding is a process that uses short DNA sequence from the standard genome for species identification. This technique is reliable and is not affected by external factors such as climates, age, or plant part. The difficulties in isolation of DNA of high quality in addition to other factors are among the challenges encountered using the DNA barcoding in the authentication of HMP. These limitations indicated that using DNA barcoding alone may ineffectively authenticate the HMP. Therefore, the combination of DNA barcoding with chromatographic fingerprint, a popular and generally accepted technique for the assessment and quality control of HMP, will offer an efficient solution to effectively evaluate the authenticity and quality consistency of HMP. Detailed and quality information about the main composition of the HMPs will help to ascertain their efficacy and safety as these are very important for quality control.
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Affiliation(s)
- Bashir Mohammed Abubakar
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
- Department of Biological Sciences, Bauchi State University Gadau, PMB 065, Bauchi, Nigeria
| | - Faezah Mohd Salleh
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir Omar
- Department of Biosciences & Health Sciences, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
| | - Alina Wagiran
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
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41
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DNA barcode and identification of the varieties and provenances of Taiwan's domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences. J Food Drug Anal 2017; 25:260-274. [PMID: 28911667 PMCID: PMC9332525 DOI: 10.1016/j.jfda.2016.06.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 01/17/2023] Open
Abstract
The major aim of made tea identification is to identify the variety and provenance of the tea plant. The present experiment used 113 tea plants [Camellia sinensis (L.) O. Kuntze] housed at the Tea Research and Extension Substation, from which 113 internal transcribed spacer 2 (ITS2) fragments, 104 trnL intron, and 98 trnL-trnF intergenic sequence region DNA sequences were successfully sequenced. The similarity of the ITS2 nucleotide sequences between tea plants housed at the Tea Research and Extension Substation was 0.379–0.994. In this polymerase chain reaction-amplified noncoding region, no varieties possessed identical sequences. Compared with the trnL intron and trnL-trnF intergenic sequence fragments of chloroplast cpDNA, the proportion of ITS2 nucleotide sequence variation was large and is more suitable for establishing a DNA barcode database to identify tea plant varieties. After establishing the database, 30 imported teas and 35 domestic made teas were used in this model system to explore the feasibility of using ITS2 sequences to identify the varieties and provenances of made teas. A phylogenetic tree was constructed using ITS2 sequences with the unweighted pair group method with arithmetic mean, which indicated that the same variety of tea plant is likely to be successfully categorized into one cluster, but contamination from other tea plants was also detected. This result provides molecular evidence that the similarity between important tea varieties in Taiwan remains high. We suggest a direct, wide collection of made tea and original samples of tea plants to establish an ITS2 sequence molecular barcode identification database to identify the varieties and provenances of tea plants. The DNA barcode comparison method can satisfy the need for a rapid, low-cost, frontline differentiation of the large amount of made teas from Taiwan and abroad, and can provide molecular evidence of their varieties and provenances.
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42
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Swetha V, Parvathy V, Sheeja T, Sasikumar B. Authentication of Myristica fragrans Houtt. using DNA barcoding. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Identification of Traditional She Medicine Shi-Liang Tea Species and Closely Related Species Using the ITS2 Barcode. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7030195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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44
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Braukmann TWA, Kuzmina ML, Sills J, Zakharov EV, Hebert PDN. Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. PLoS One 2017; 12:e0169515. [PMID: 28072819 PMCID: PMC5224991 DOI: 10.1371/journal.pone.0169515] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/18/2016] [Indexed: 01/30/2023] Open
Abstract
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest.
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Affiliation(s)
- Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Maria L. Kuzmina
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jesse Sills
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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Shi Y, Zhao M, Yao H, Yang P, Xin T, Li B, Sun W, Chen S. Rapidly discriminate commercial medicinal Pulsatilla chinensis (Bge.) Regel from its adulterants using ITS2 barcoding and specific PCR-RFLP assay. Sci Rep 2017; 7:40000. [PMID: 28059130 PMCID: PMC5216359 DOI: 10.1038/srep40000] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 12/01/2016] [Indexed: 12/18/2022] Open
Abstract
Pulsatillae radix is a conventional traditional Chinese medicine (TCM) with common name Baitouweng, and has notable effects on inflammation and dysentery. Pulsatilla chinensis (Bge.) Regel is the only source plant of Baitouweng recorded in Chinese Pharmacopoeia, but its adulteration often occurs in the market that possibly affects medicinal efficacy and safety. We have established an internal transcribed spacer 2 (ITS2) barcode library based on 105 plant samples from 12 Pulsatilla species and 10 common adulterants. Results indicate that ITS2 barcoding can accurately distinguish Pulsatilla species from their adulterants. Pulsatilla chinensis can be discriminated from 11 congeneric species by two stable single nucleotide polymorphisms (SNPs) in the ITS2 region. Additionally, a quick specific PCR-RFLP identification assay based on the ITS2 barcode was developed. Using specific primers ITS2/PR1 combined with restriction enzyme Bgl I, Pu. chinensis can rapidly be differentiated from other species via simple and low-cost test procedures. Furthermore, 30 commercial Baitouweng products were tested and only two products were derived from authentic Pu. chinensis. Thus, these two molecular approaches provide practical tools for quick identification of commercial Baitouweng products and can help ensure the safe use of this TCM product.
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Affiliation(s)
- Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mingming Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Pei Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Tianyi Xin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Bin Li
- Xi'an Botanical Garden of Shanxi Province, Xi'an 710061, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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Horn T, Häser A. Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data. PeerJ 2016; 4:e2781. [PMID: 27957401 PMCID: PMC5149056 DOI: 10.7717/peerj.2781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/10/2016] [Indexed: 11/30/2022] Open
Abstract
Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.
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Affiliation(s)
- Thomas Horn
- Molecular Cellbiology, Karlsruhe Institute of Technology , Karlsruhe , Germany
| | - Annette Häser
- Molecular Cellbiology, Karlsruhe Institute of Technology , Karlsruhe , Germany
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Fluorescence Visual Detection of Herbal Product Substitutions at Terminal Herbal Markets by CCP-based FRET technique. Sci Rep 2016; 6:35540. [PMID: 27765955 PMCID: PMC5073245 DOI: 10.1038/srep35540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022] Open
Abstract
Inaccurate labeling of materials used in herbal products may compromise the therapeutic efficacy and may pose a threat to medicinal safety. In this paper, a rapid (within 3 h), sensitive and visual colorimetric method for identifying substitutions in terminal market products was developed using cationic conjugated polymer-based fluorescence resonance energy transfer (CCP-based FRET). Chinese medicinal materials with similar morphology and chemical composition were clearly distinguished by the single-nucleotide polymorphism (SNP) genotyping method. Assays using CCP-based FRET technology showed a high frequency of adulterants in Lu-Rong (52.83%) and Chuan-Bei-Mu (67.8%) decoction pieces, and patented Chinese drugs (71.4%, 5/7) containing Chuan-Bei-Mu ingredients were detected in the terminal herbal market. In comparison with DNA sequencing, this protocol simplifies procedures by eliminating the cumbersome workups and sophisticated instruments, and only a trace amount of DNA is required. The CCP-based method is particularly attractive because it can detect adulterants in admixture samples with high sensitivity. Therefore, the CCP-based detection system shows great potential for routine terminal market checks and drug safety controls.
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48
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Nithaniyal S, Vassou SL, Poovitha S, Raju B, Parani M. Identification of species adulteration in traded medicinal plant raw drugs using DNA barcoding. Genome 2016; 60:139-146. [PMID: 28067539 DOI: 10.1139/gen-2015-0225] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Plants are the major source of therapeutic ingredients in complementary and alternative medicine (CAM). However, species adulteration in traded medicinal plant raw drugs threatens the reliability and safety of CAM. Since morphological features of medicinal plants are often not intact in the raw drugs, DNA barcoding was employed for species identification. Adulteration in 112 traded raw drugs was tested after creating a reference DNA barcode library consisting of 1452 rbcL and matK barcodes from 521 medicinal plant species. Species resolution of this library was 74.4%, 90.2%, and 93.0% for rbcL, matK, and rbcL + matK, respectively. DNA barcoding revealed adulteration in about 20% of the raw drugs, and at least 6% of them were derived from plants with completely different medicinal or toxic properties. Raw drugs in the form of dried roots, powders, and whole plants were found to be more prone to adulteration than rhizomes, fruits, and seeds. Morphological resemblance, co-occurrence, mislabeling, confusing vernacular names, and unauthorized or fraudulent substitutions might have contributed to species adulteration in the raw drugs. Therefore, this library can be routinely used to authenticate traded raw drugs for the benefit of all stakeholders: traders, consumers, and regulatory agencies.
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Affiliation(s)
- Stalin Nithaniyal
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Sophie Lorraine Vassou
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Sundar Poovitha
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Balaji Raju
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Madasamy Parani
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
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Estimating Herbal Product Authentication and Adulteration in India Using a Vouchered, DNA-Based Biological Reference Material Library. Drug Saf 2016; 39:1211-1227. [DOI: 10.1007/s40264-016-0459-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Hollingsworth PM, Li DZ, van der Bank M, Twyford AD. Telling plant species apart with DNA: from barcodes to genomes. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150338. [PMID: 27481790 PMCID: PMC4971190 DOI: 10.1098/rstb.2015.0338] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 12/17/2022] Open
Abstract
Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, Yunnan 650201, People's Republic of China
| | - Michelle van der Bank
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland park, Johannesburg PO Box 524, South Africa
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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