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      Determining the Authenticity of Shark Meat Products by DNA Sequencing

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          Abstract

          Given that the global shark meat market is poised to grow in future years, the aim of this study was to use DNA sequencing of the cytochrome c oxidase I (COI) and NADH dehydrogenase subunit 2 (NADH2) mitochondrial genes to examine the market of shark meat products in Italy. This made it possible to analyze patterns of species utilization and commercialization of threatened, endangered and/or prohibited species, focusing on fraudulent activities in the shark food chain in order to propose seafood safety and environmental sustainability solutions. The study shows that the labeling of shark meat products generally lacks comprehensive information, thus making it difficult for consumers to make informed purchasing decisions and fails to comply with European Union (EU) legislation regarding seafood labelling. Molecular investigation reveals a high mislabeling rate (45.4%), highlighting widespread use of cheaper species either in order to replace species that are better known and more popular, or else in order to sell various threatened species. Considering that seafood mislabeling can circumvent the management of sustainable fisheries and facilitate Illegal, Unreported and Unregulated (IUU) fishing, the routine use of genetic analysis should be encouraged among control and enforcement agencies in order to implement effective management measures. This would help to build a species-specific reporting system for all catches, and enhance control measures, in order to prevent illegal activities connected with shark catches and trade around the world.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

            Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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              IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

              Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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                Author and article information

                Journal
                Foods
                Foods
                foods
                Foods
                MDPI
                2304-8158
                28 August 2020
                September 2020
                : 9
                : 9
                : 1194
                Affiliations
                [1 ]Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano (Bari), Italy; patrizia.marchetti@ 123456uniba.it (P.M.); anna.mottola@ 123456uniba.it (A.M.)
                [2 ]Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; robpiredda@ 123456gmail.com
                [3 ]Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, S.S. 7 ter, km 73, Zona Industriale, 73012 Campi Salentina (LE), Italy; giuseppina.ciccarese@ 123456izspb.it
                Author notes
                [* ]Correspondence: angela.dipinto@ 123456uniba.it ; Tel.: +390-804-679-878; Fax: +390-805-443-855
                Author information
                https://orcid.org/0000-0002-6932-907X
                https://orcid.org/0000-0002-6672-439X
                https://orcid.org/0000-0003-4002-8748
                https://orcid.org/0000-0001-7755-9724
                Article
                foods-09-01194
                10.3390/foods9091194
                7555804
                32872285
                5fc2cf4a-1218-44f0-b09b-f97c0c109771
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 23 July 2020
                : 26 August 2020
                Categories
                Article

                shark meat products,dna sequencing,species identification,food authenticity,food safety,mislabeling,fishery regulations,environmental sustainability,traceability

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