A multiplex PCR mini-barcode assay to identify processed shark products in the global trade

Diego Cardeñosa,Andrew Fields,Debra Abercrombie,Stanley K H Shea,Demian D Chapman,Kevin Feldheim,Mehrdad Hajibabaei

doi:10.1371/journal.pone.0185368

Diego Cardeñosa, Andrew Fields + Show 5 more

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https://doi.org/10.1371/journal.pone.0185368

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Abstract

Protecting sharks from overexploitation has become global priority after widespread population declines have occurred. Tracking catches and trade on a species-specific basis has proven challenging, in part due to difficulties in identifying processed shark products such as fins, meat, and liver oil. This has hindered efforts to implement regulations aimed at promoting sustainable use of commercially important species and protection of imperiled species. Genetic approaches to identify shark products exist but are typically based on sequencing or amplifying large DNA regions and may fail to work on heavily processed products in which DNA is degraded. Here, we describe a novel multiplex PCR mini-barcode assay based on two short fragments of the cytochrome oxidase I (COI) gene. This assay can identify to species all sharks currently listed on the Convention of International Trade of Endangered Species (CITES) and most shark species present in the international trade. It achieves species diagnosis based on a single PCR and one to two downstream DNA sequencing reactions. The assay is capable of identifying highly processed shark products including fins, cooked shark fin soup, and skin-care products containing liver oil. This is a straightforward and reliable identification method for data collection and enforcement of regulations implemented for certain species at all governance levels.

Highlights

Monitoring the international trade of wildlife has become a priority for most countries, enforcement is challenging due to the lack of appropriate and cost-effective implementation tools [1]
A multiplex PCR mini-barcode assay to identify processed shark products in the global trade proper documentation certifying that products being traded were sustainably and legally taken from the wild (Rhincodon typus (2001), Cetorhinus maximus (2001), Carcharodon carcharias (2004), Carcharhinus longimanus (2013), Lamna nasus (2013), Sphyrna lewini (2013), S. mokarran (2013), S. zygaena (2013; [7]), Carcharhinus falciformis (2016), Alopias superciliosus (2016), A. pelagicus (2016), and A. vulpinus (2016))
Beyond the enforcement of Convention of International Trade of Endangered Species (CITES) regulations there are many other monitoring and law enforcement contexts where it may be necessary to identify shark species, for example when certain species are prohibited in a fishery (e.g. [8]) or when landings must be tracked by species in order to keep them below catch limits

Summary

Introduction

Monitoring the international trade of wildlife has become a priority for most countries, enforcement is challenging due to the lack of appropriate and cost-effective implementation tools [1]. Many other shark products such as liver oil, salted meat, and some processed fins cannot be visually identified to species and contain highly degraded genomic DNA that reduces amplification and sequencing success for genetic identification.

Results

Conclusion