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.
Highlights
Genetic identification of species plays a key role in the investigation of illegal trade of protected or endangered wildlife [1] and in the detection of species mislabelling and fraud in the food industry [2]
DNA barcoding is being used by the US Food and Drug Administration as a replacement for the time-consuming technique of protein isoelectric focusing for fish and fish products [6]
Validation of the approach should be performed before DNA metabarcoding can be applied in a routine setup
Summary
Genetic identification of species plays a key role in the investigation of illegal trade of protected or endangered wildlife [1] and in the detection of species mislabelling and fraud in the food industry [2]. Mini-barcodes based on the 12S and 16S rDNA mitochondrial genes have recently been demonstrated by several studies to be suited for identifying a wide range of animal species in environmental samples [89] and processed food and wildlife forensic products including TMs [21, 23, 73, 76]. Forensic samples are often heavily processed and may contain severely fragmented DNA, hampering the ability to PCR amplify full-length barcodes In such cases, mini-barcodes are often the only alternative, but these do not always provide species-level resolution, and truly universal primers for mini-barcode amplification have been found difficult to design. Several dedicated software tools have been developed, but there is a need to validate pipelines for clustering of reads into OTUs, using benchmarked algorithms for quality control, denoising, chimera removal and OTU picking
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