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Yanqing C, Bo W, Ping W, Bisheng H, Hegang L, Chao X, Mingli W, Nili W, Di L, Zhigang H, Shilin C. Rapid identification of common medicinal snakes and their adulterants using the Bar-HRM analysis method. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:367-374. [PMID: 30686100 DOI: 10.1080/24701394.2018.1532417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Effective identification methods for snake species are lacking, exacerbating the extermination of medicinal and commercially valuable snake species. Hence, it is imperative to find fast and reliable methods to distinguish snake samples available on the market. Seventy-three samples from four families belonging to 13 genera were collected in China and found to contain common medicinal snakes and their adulterants. Cytochrome oxidase I (COI) was utilized as a DNA barcode to analyse these common snakes, and a DNA mini-barcode was employed for fast detection. Then, the DNA mini-barcode assays were coupled with a high-resolution melting (HRM) analysis (Bar-HRM) to realize the rapid discrimination of these snake species. The results showed the power of DNA barcoding with COI, which was capable of distinguishing all collected snake samples, and the combined Bar-HRM method can successfully identify the adulterants and different snake species. In particular, Bar-HRM revealed Bungarus fasciatus adulterants in B. multicinctus at concentrations as low as 1.6%. Moreover, the results of the study confirmed the effectiveness of the technique in terms of the rapid identification of snakes, which has great potential for ensuring the safety of commercially valuable snake species.
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Affiliation(s)
- Chen Yanqing
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China
| | - Wang Bo
- b Hubei Institute for Drug Control , Wuhan , China
| | - Wang Ping
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China
| | - Huang Bisheng
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China
| | - Liu Hegang
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China.,c Zhan Yahua National Famous Traditional Chinese Medicine Experts Inheritance Studio , Wuhan , China
| | - Xiong Chao
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China
| | - Wu Mingli
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China
| | - Wang Nili
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China
| | - Liu Di
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China.,c Zhan Yahua National Famous Traditional Chinese Medicine Experts Inheritance Studio , Wuhan , China
| | - Hu Zhigang
- a College of Pharmacy , Hubei University of Chinese Medicine , Wuhan , China.,c Zhan Yahua National Famous Traditional Chinese Medicine Experts Inheritance Studio , Wuhan , China
| | - Chen Shilin
- d Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing , China
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Arulandhu AJ, Staats M, Hagelaar R, Voorhuijzen MM, Prins TW, Scholtens I, Costessi A, Duijsings D, Rechenmann F, Gaspar FB, Barreto Crespo MT, Holst-Jensen A, Birck M, Burns M, Haynes E, Hochegger R, Klingl A, Lundberg L, Natale C, Niekamp H, Perri E, Barbante A, Rosec JP, Seyfarth R, Sovová T, Van Moorleghem C, van Ruth S, Peelen T, Kok E. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples. Gigascience 2018; 6:1-18. [PMID: 29020743 PMCID: PMC5632295 DOI: 10.1093/gigascience/gix080] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/15/2017] [Indexed: 11/19/2022] Open
Abstract
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.
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Affiliation(s)
- Alfred J Arulandhu
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Martijn Staats
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Rico Hagelaar
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Marleen M Voorhuijzen
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Theo W Prins
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Ingrid Scholtens
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Danny Duijsings
- Baseclear B. V, Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - François Rechenmann
- GenoStar Bioinformatics Solutions, 60 rue Lavoisier, 38330 Montbonnot Saint Martin, France
| | - Frédéric B Gaspar
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | | | - Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106 Oslo, Norway
| | - Matthew Birck
- U.S. Customs and Border Protection Laboratory, 1100 Raymond Blvd Newark, NJ 07102 USA
| | - Malcolm Burns
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK
| | | | - Rupert Hochegger
- Austrian Agency for Health and Food Safety, Spargelfeldstrasse 191, 1220 Vienna, Austria
| | - Alexander Klingl
- Generalzolldirektion, Direktion IX, Bildungs- und Wissenschaftszentrum der Bundesfinanzverwaltung, Dienstort Hamburg, Baumacker 3, D-22523 Hamburg, Germany
| | - Lisa Lundberg
- Livsmedelsverket, Att. Lisa Lundberg, Strandbodgatan 4, SE 75323 Uppsala, Sweden
| | - Chiara Natale
- AGENZIA DELLE DOGANE E DEI MONOPOLI, Laboratori e servizi chimici - Laboratorio Chimico di Genova, 16126 Genova, Via Rubattino n. 6, Italy
| | - Hauke Niekamp
- Eurofins GeneScan GmbH, Engesserstrasse 4 79108 Freiburg, Germany
| | - Elena Perri
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Alessandra Barbante
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Jean-Philippe Rosec
- Service Commun des Laboratoires, Laboratoire de Montpellier, Parc Euromédecine, 205 rue de la Croix Verte, 34196 Montpellier Cedex 5, France
| | - Ralf Seyfarth
- Biolytix AG, Benkenstrasse 254, 4108 Witterswil, Switzerland
| | - Tereza Sovová
- Crop Research Institute, Department of Molecular Genetics, Drnovská 507, 161 06 Prague, Czech Republic
| | | | - Saskia van Ruth
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Tamara Peelen
- Dutch Customs Laboratory, Kingsfordweg 1, 1043 GN, Amsterdam, The Netherlands
| | - Esther Kok
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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