Nuclear DNA barcodes for cod identification in mildly-treated and processed food products

References

• Asensio Gil L. 2007. PCR-based methods for fish and fishery products authentication. Trends Food Sci Technol. 18(11):558–566.
   Web of Science ®Google Scholar
• Cawthorn DM, Steinman HA, Witthuhn RC. 2011. Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa. Mol Ecol Resour. 11(6):979–991.
   PubMed Web of Science ®Google Scholar
• Clark LF. 2015. The current status of DNA barcoding technology for species identification in fish value chains. Food Policy. 54(SupplementC):85–94.
   Google Scholar
• Cline SD. 2012. Mitochondrial DNA damage and its consequences for mitochondrial gene expression. Biochim Biophys Acta. 1819(9–10):979–991.
   PubMed Web of Science ®Google Scholar
• Cutarelli A, Amoroso MG, De Roma A, Girardi S, Galiero G, Guarino A, Corrado F. 2014. Italian market fish species identification and commercial frauds revealing by DNA sequencing. Food Control. 37(SupplementC):46–50.
   Google Scholar
• Dalmasso A, Chiesa F, Civera T, Bottero MT. 2013. A novel minisequencing test for species identification of salted and dried products derived from species belonging to Gadiformes. Food Control. 34(2):296–299.
   Web of Science ®Google Scholar
• Di Pinto A, Di Pinto P, Terio V, Bozzo G, Bonerba E, Ceci E, Tantillo G. 2013. DNA barcoding for detecting market substitution in salted cod fillets and battered cod chunks. Food Chem. 141(3):1757–1762.
   PubMed Web of Science ®Google Scholar
• Everstine K, Spink J, Kennedy S. 2013. Economically motivated adulteration (EMA) of food: common characteristics of EMA incidents. J Food Prot. 76(4):723–735.
   PubMed Web of Science ®Google Scholar
• [FAO] Food and Agriculture Organization. 2014. The state of world fisheries and aquaculture 2014. http://www.fao.org/3/a-i3720e.pdf.
   Google Scholar
• Fernandes TJR, Costa J, Oliveira MBPP, Mafra I. 2018. COI barcode-HRM as a novel approach for the discrimination of hake species. Fisheries Research. 197:50–59.
   Web of Science ®Google Scholar
• Fernandes TJR, Silva CR, Costa J, Oliveira MBPP, Mafra I. 2017. High resolution melting analysis of a COI mini-barcode as a new approach for Penaeidae shrimp species discrimination. Food Control. 82(SupplementC):8–17.
   Google Scholar
• Ferrito V, Bertolino V, Pappalardo AM. 2016. White fish authentication by COIBar-RFLP: toward a common strategy for the rapid identification of species in convenience seafood. Food Control. 70(SupplementC):130–137.
   Google Scholar
• Filonzi L, Chiesa S, Vaghi M, Nonnis Marzano F. 2010. Molecular barcoding reveals mislabelling of commercial fish products in Italy. Food Res Int. 43(5):1383–1388.
   Web of Science ®Google Scholar
• Garcia-Vazquez E, Perez J, Martinez JL, Pardinas AF, Lopez B, Karaiskou N, Casa MF, Machado-Schiaffino G, Triantafyllidis A. 2011. High level of mislabeling in Spanish and Greek hake markets suggests the fraudulent introduction of African species. J Agric Food Chem. 59(2):475–480.
   PubMed Web of Science ®Google Scholar
• Gordon A, Hannon GJ Forthcoming 2010. Fastx-toolkit. FASTQ/A Short-Reads Preprocessing Tools (unpublished) http://hannonlab.Cshl.Edu/fastx_toolkit.
   Google Scholar
• Griffiths AM, Sotelo CG, Mendes R, Pérez-Martín RI, Schröder U, Shorten M, Silva HA, Verrez-Bagnis V, Mariani S. 2014. Current methods for seafood authenticity testing in Europe: is there a need for harmonisation? Food Control. 45:95–100.
   Web of Science ®Google Scholar
• Hebert PD, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc Biol Sci. 270(1512):313–321.
   PubMed Web of Science ®Google Scholar
• Hellberg RS, Kawalek MD, Van KT, Shen Y, Williams-Hill DM. 2014. Comparison of DNA extraction and PCR setup methods for use in high-throughput DNA Barcoding of fish species [journal article]. Food Anal Methods. 7(10):1950–1959.
   Web of Science ®Google Scholar
• Helyar SJ, HaD L, de Bruyn M, Leake J, Bennett N, Carvalho GR. 2014. Fish product mislabelling: Failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) Fishing. PLoS ONE. 9(6):e98691.
   PubMed Web of Science ®Google Scholar
• Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. 2007. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes. 7(4):544–548.
   Google Scholar
• Jacquet J, Pauly D. 2008. Funding priorities: big barriers to small-scale fisheries. Conserv Biol. 22(4):832–835.
   PubMed Web of Science ®Google Scholar
• Khaksar R, Carlson T, Schaffner DW, Ghorashi M, Best D, Jandhyala S, Traverso J, Amini S. 2015. Unmasking seafood mislabeling in U.S. markets: DNA barcoding as a unique technology for food authentication and quality control. Food Control. 56:71–76.
   Web of Science ®Google Scholar
• Martin M. 2011 May. Cutadapt removes adapter sequences from high-throughput sequencing reads EMBnet. journal, [S.l.], 17(1):10–12. ISSN 2226–6089. Accessed: 2018 Dec 11. doi:https://doi.org/10.14806/ej.17.1.200.
   Google Scholar
• Mazzeo MF, Siciliano RA. 2016. Proteomics for the authentication of fish species. J Proteomics. 147:119–124.
   PubMed Web of Science ®Google Scholar
• Miller D, Jessel A, Mariani S. 2012. Seafood mislabelling: comparisons of two western European case studies assist in defining influencing factors, mechanisms and motives. Fish and Fisheries. 13(3):345–358.
   Web of Science ®Google Scholar
• Miller DD, Mariani S. 2010. Smoke, mirrors, and mislabeled cod: poor transparency in the European seafood industry. Front Ecol Environ. 8(10):517–521.
   Web of Science ®Google Scholar
• Mendes R, Silva H. 2015. Control of seafood labelling in Portugal. Relatório Científico e Técnico do IPMA. p. 1–17.
   Google Scholar
• Mueller S, Handy SM, Deeds JR, George GO, Broadhead WJ, Pugh SE, Garrett SD. 2015. Development of a COX1 based PCR-RFLP method for fish species identification. Food Control. 55:39–42.
   Web of Science ®Google Scholar
• Nedunoori A, Turanov SV, Kartavtsev YP. 2017. Fish product mislabeling identified in the Russian far east using DNA barcoding. Gene Reports. 8(SupplementC):144–149.
   Google Scholar
• Paracchini V, Petrillo M, Lievens A, Puertas Gallardo A, Martinsohn JT, Hofherr J, Maquet A, Silva APB, Kagkli DM, Querci M, et al. 2017. Novel nuclear barcode regions for the identification of flatfish species. Food Control. 79:297–308.
   PubMed Web of Science ®Google Scholar
• Pepe T, Trotta M, Di Marco I, Anastasio A, Bautista JM, Cortesi ML. 2007. Fish species identification in surimi-based products. J Agric Food Chem. 55(9):3681–3685.
   PubMed Web of Science ®Google Scholar
• Rasmussen RS, Morrissey MT. 2008. DNA-based methods for the identification of commercial fish and seafood species. Compr Rev Food Sci Food Saf. 7(3):280–295.
   PubMed Web of Science ®Google Scholar
• Ratnasingham S, Hebert PDN. 2007. The Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes. 7(3):355–364.
   Google Scholar
• European Union. 2011. Regulation (EU). No 1169/2011. http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2011:304:0018:0063:en:PDF
   Google Scholar
• European Union. 2013. Regulation (EU). No 1379/2013. http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2013:354:0001:0021:EN:PDF
   Google Scholar
• Rehbein H. 2013. Differentiation of fish species by PCR-based DNA analysis of nuclear genes. Eur Food Res Technol. 236(6):979–990.
   Web of Science ®Google Scholar
• Saull J, Duggan C, Hobbs G, Edwards T. 2016. The detection of Atlantic cod (Gadus morhua) using loop mediated isothermal amplification in conjunction with a simplified DNA extraction process. Food Control. 59(SupplementC):306–313.
   Google Scholar
• Strauss RE, Bond CE. 1990. Taxonomic methods: Morphology. In: Schreck CB, Moyle, editors. Methods for fish biology. American Fisheries Society; Bethesda, Maryland, p. 109–140.
   Google Scholar
• Tomás C, Ferreira IMPLVO, Faria MA. 2017. Codfish authentication by a fast Short Amplicon High Resolution Melting Analysis (SA-HRMA) method. Food Control. 71(SupplementC):255–263.
   Google Scholar
• Triantafyllidis A, Karaiskou N, Perez J, Martinez JL, Roca A, Lopez B, Garcia-Vazquez E. 2010. Fish allergy risk derived from ambiguous vernacular fish names: forensic DNA-based detection in Greek markets. Food Res Int. 43(8):2214–2216.
   Web of Science ®Google Scholar
• [US FDA] US Food and Drug Administration. 2014. Seafood species substitution and economic fraud. http://www.fda.gov/Food/FoodScienceResearch/RFE/ucm071528.htm.
   Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci. 360(1462):1847–1857.
   PubMed Web of Science ®Google Scholar
• Watanabe ME. 2013. Assembling an online tree of life of two million species. Bioscience. 63(1):64.
   Google Scholar
• Xiong X, D’Amico P, Guardone L, Castigliego L, Guidi A, Gianfaldoni D, Armani A. 2016. The uncertainty of seafood labeling in China: A case study on Cod, Salmon and Tuna. Marine Policy. 68(SupplementC):123–135.
   Google Scholar