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      Advances in DNA metabarcoding for food and wildlife forensic species identification

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          Abstract

          Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders’ needs.

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          AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

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            Universal primers for amplification of three non-coding regions of chloroplast DNA.

            Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
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              A DNA barcode for land plants.

              DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
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                Author and article information

                Contributors
                martijn.staats@wur.nl
                Journal
                Anal Bioanal Chem
                Anal Bioanal Chem
                Analytical and Bioanalytical Chemistry
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                1618-2642
                1618-2650
                13 May 2016
                13 May 2016
                2016
                : 408
                : 4615-4630
                Affiliations
                [ ]RIKILT Wageningen UR, P.O. Box 230, 6700 AE Wageningen, The Netherlands
                [ ]Naturalis Biodiversity Center, Sylviusweg 72, P.O. Box 9517, Leiden, The Netherlands
                [ ]Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106 Oslo Norway
                [ ]Dutch Customs Laboratory, Kingsfordweg 1, 1043 GN Amsterdam, The Netherlands
                Article
                9595
                10.1007/s00216-016-9595-8
                4909793
                27178552
                0b13e58e-9d4f-499b-9528-a588cf33ccbb
                © The Author(s) 2016

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                History
                : 10 February 2016
                : 19 April 2016
                : 20 April 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100004963, Seventh Framework Programme;
                Award ID: FP7-KBBE-2013-7-613908-Decathlon
                Categories
                Review
                Custom metadata
                © Springer-Verlag Berlin Heidelberg 2016

                Analytical chemistry
                endangered species,next-generation sequencing,wildlife forensic samples,cytochrome c oxidase i,convention on international trade of endangered species

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