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Development of a DNA Metabarcoding Method for the Identification of Bivalve Species in Seafood Products. Foods 2021; 10:foods10112618. [PMID: 34828894 PMCID: PMC8617786 DOI: 10.3390/foods10112618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
The production of bivalve species has been increasing in the last decades. In spite of strict requirements for species declaration, incorrect labelling of bivalve products has repeatedly been detected. We present a DNA metabarcoding method allowing the identification of bivalve species belonging to the bivalve families Mytilidae (mussels), Pectinidae (scallops), and Ostreidae (oysters) in foodstuffs. The method, developed on Illumina instruments, targets a 150 bp fragment of mitochondrial 16S rDNA. We designed seven primers (three primers for mussel species, two primers for scallop species and a primer pair for oyster species) and combined them in a triplex PCR assay. In each of eleven reference samples, the bivalve species was identified correctly. In ten DNA extract mixtures, not only the main component (97.0-98.0%) but also the minor components (0.5-1.5%) were detected correctly, with only a few exceptions. The DNA metabarcoding method was found to be applicable to complex and processed foodstuffs, allowing the identification of bivalves in, e.g., marinated form, in sauces, in seafood mixes and even in instant noodle seafood. The method is highly suitable for food authentication in routine analysis, in particular in combination with a DNA metabarcoding method for mammalian and poultry species published recently.
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Vincenzetti S, Felici A, Ciarrocchi G, Pucciarelli S, Ricciutelli M, Ariani A, Polzonetti V, Polidori P. Comparative proteomic analysis of two clam species: Chamelea gallina and Tapes philippinarum. Food Chem 2017; 219:223-229. [PMID: 27765220 DOI: 10.1016/j.foodchem.2016.09.150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 09/08/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022]
Abstract
Clams have long been a fisheries and aquaculture sector of great importance in Italy, the main resource of fisheries is the Chamelea gallina of indigenous origin, whereas clams breeding is supported almost entirely by the Tapes philippinarum, a species of Indo-Pacific origin. Bivalve molluscs quality depends mainly on the water quality, and then by a series of factors such as water temperature and salinity, gametogenic cycle, food availability, and environmental conditions, that affect the Condition Index. In this work crude extracts obtained from the edible part of Chamelea gallina and Tapes philippinarum were analyzed by a proteomic approach based on a two-dimensional gel electrophoresis followed by liquid chromatography-tandem mass spectrometry, in order to detect biomarkers useful for identification of the two kinds of clams and to assess their nutritional characteristics. As a result, four differentially expressed spots were found and identified, namely enolase, cyclophilin-A, ribosomal protein L13 and actin-1.
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Affiliation(s)
- Silvia Vincenzetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy.
| | - Alberto Felici
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Giorgio Ciarrocchi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Stefania Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | | | - Ambra Ariani
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Valeria Polzonetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Paolo Polidori
- School of Pharmacy, University of Camerino, Camerino (MC), Italy
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Abbadi M, Marciano S, Tosi F, De Battisti C, Panzarin V, Arcangeli G, Cattoli G. Species identification of bivalve molluscs by pyrosequencing. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:512-519. [PMID: 27068666 DOI: 10.1002/jsfa.7754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/23/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The increase in seafood consumption and the presence of different species of bivalves on the global markets has given rise to several commercial frauds based on species substitution. To prevent and detect wilful or unintentional frauds, reliable and rapid techniques are required to identify seafood species in different products. In the present work, a pyrosequencing-based technology has been used for the molecular identification of bivalve species. RESULTS Processed and unprocessed samples of 15 species belonging to the bivalve families Pectinidae, Mytilidae, Donacidae, Ostreidae, Pharide and Veneridae were analysed and correctly identified by the developed pyrosequencing-based method according to the homology between query sequences of the 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase I (COI) genes and their correspondent reference libraries. This technique exhibits great potential in automated and high-throughput processing systems, allowing the simultaneous analysis of 96 samples in shorter execution and turnaround times. CONCLUSIONS The correct identification of all the species shows how useful this technique may prove to differentiate species from different products, providing an alternative, simple, rapid and economical tool to detect seafood substitution frauds. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Miriam Abbadi
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Sabrina Marciano
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Federica Tosi
- National Reference Laboratory for Fish, Molluscs and Crustacean Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, 45011 Adria, Rovigo, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Cristian De Battisti
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Valentina Panzarin
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Giuseppe Arcangeli
- National Reference Laboratory for Fish, Molluscs and Crustacean Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, 45011 Adria, Rovigo, Italy
| | - Giovanni Cattoli
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
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Kim EM, Byun SG, An CM, Kang JH, An HS, Dong CM, Kim MJ, Hong YK, Park JY. Development of single nucleotide polymorphism markers from ESTs for discrimination between domestic and imported manila clams, Ruditapes philippinarum. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Cho YA, Kim EM, Kim MJ, Kang JH, Dong CM, An HS, An CM, Park MA, Park JY. A rapid and simple method for distinguishing two mitten crabs (Eriocheir sinensis and Eriocheir japonica) in Korea using PCR-RFLP and PCR. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.07.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sanna D, Dedola GL, Lai T, Curini-Galletti M, Casu M. PCR-RFLP: A practical method for the identification of specimens ofPatella ulyssiponensis s.l.(Gastropoda: Patellidae). ACTA ACUST UNITED AC 2012. [DOI: 10.1080/11250003.2011.620988] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Genetic variation and population structure of the carpet shell clam Ruditapes decussatus along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis. Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0069-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Rasmussen RS, Morrissey MT. Application of DNA-Based Methods to Identify Fish and Seafood Substitution on the Commercial Market. Compr Rev Food Sci Food Saf 2009. [DOI: 10.1111/j.1541-4337.2009.00073.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Espiñeira M, González-Lavín N, Vieites JM, Santaclara FJ. Development of a method for the genetic identification of commercial bivalve species based on mitochondrial 18S rRNA sequences. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:495-502. [PMID: 19128038 DOI: 10.1021/jf802787d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study a genetic methodology based on the amplification of an 18S rRNA fragment by PCR and phylogenetic analysis of the obtained DNA sequences was developed. This technique allows the genetic identification of more than 50 bivalve species in fresh, frozen, precooked and canned products. The developed method was applied to 30 commercial samples to check their labeling, showing that 12 samples were incorrectly labeled (40%). Therefore, the proposed methodology is appropriate to study questions related to the correct labeling and traceability of commercial products and the control of imported bivalves and fisheries in order to guarantee the protection of consumers' rights and verify the transparency of the extractive and transforming industries.
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Rasmussen RS, Morrissey MT. DNA-Based Methods for the Identification of Commercial Fish and Seafood Species. Compr Rev Food Sci Food Saf 2008; 7:280-295. [PMID: 33467804 DOI: 10.1111/j.1541-4337.2008.00046.x] [Citation(s) in RCA: 230] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The detection of species substitution has become an important topic within the food industry and there is a growing need for rapid, reliable, and reproducible tests to verify species in commercial fish and seafood products. Increases in international trade and global seafood consumption, along with fluctuations in the supply and demand of different fish and seafood species, have resulted in intentional product mislabeling. The effects of species substitution are far-reaching and include economic fraud, health hazards, and illegal trade of protected species. To improve detection of commercial seafood fraud, a variety of DNA-based techniques have been developed, including Multiplex PCR, FINS, PCR-RFLP, PCR-RAPD, PCR-AFLP, and PCR-SSCP, which are all based on polymorphisms in the genetic codes of different species. These techniques have been applied in the differentiation of many types of fish and seafood species, such as gadoids, salmonids, scombroids, and bivalves. Some emerging technologies in this field include the use of real-time PCR, lab-on-a-chip, and DNA microarray chips. In this review article, the major DNA-based methods currently employed in the authentication of commercial fish and seafood species are discussed and future trends are highlighted. Examples of commercial applications and the use of online database resources are also considered.
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Affiliation(s)
- Rosalee S Rasmussen
- Author Rasmussen is with Dept. of Food Science and Technology, OSU Seafood Laboratory, Oregon State Univ., 2001 Marine Dr., Room 253, Astoria, OR 97103, U.S.A. Author Morrissey is with Oregon State University Food Innovation Center, 1207 NW Naito Parkway, Portland, OR 97209, U.S.A. Direct inquiries to author Morrissey (E-mail: )
| | - Michael T Morrissey
- Author Rasmussen is with Dept. of Food Science and Technology, OSU Seafood Laboratory, Oregon State Univ., 2001 Marine Dr., Room 253, Astoria, OR 97103, U.S.A. Author Morrissey is with Oregon State University Food Innovation Center, 1207 NW Naito Parkway, Portland, OR 97209, U.S.A. Direct inquiries to author Morrissey (E-mail: )
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Abstract
Tetrodotoxin (TTX) is one of the most potent and oldest known neurotoxins. The poisoning cases due to ingestion of TTX-containing marine animals, especially for puffer, have frequently occurred in Asia since a long time ago. This chapter describes various topics on TTX poisoning including the tendency of poisoning incidents, typical case report, treatment and prevention, biology distribution, original source, infestation mechanism, detection methods, characteristics of chemistry and pharmacology, and therapeutic application. Furthermore, the protocols for how to make puffer safe to eat and how to prevent puffer products made from toxic puffers have been suggested. Finally, the biological significance and neurophysiological role of TTX have been elucidated and TTX may act as an important drug like anesthetic in future.
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Affiliation(s)
- Deng-Fwu Hwang
- Department of Food Science, National Taiwan Ocean University Taiwan, Taiwan, Republic of China
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Abstract
A simple and reliable method was developed for extracting genomic DNA from preserved mantle tissues of Pacific oyster Crassostrea gigas for reproducible PCR amplification. The method was based on destruction of the tissue using Proteinase K, Chelex 100 resin, detergents, and urea, followed by preferential capturing of genomic DNA with silica particles. Approximately 5 mg of mantle tissue provided a sufficient quality and quantity of DNA for several hundreds of PCR reactions amplifying the hypervariable mitochondrial DNA intergenic spacer, which is a useful genetic marker for population structure analysis of Pacific oyster. The method can be applied for DNA preparation from not only fresh and frozen but also ethanol-preserved mantle tissues, so this rapid and economical method can serve for investigating a large number of bivalve specimens collected in the field and next transported in ethanol at ambient temperature.
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Affiliation(s)
- Futoshi Aranishi
- Department of Biological and Environmental Sciences, Miyazaki University, Miyazaki 889-2192, Japan.
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Abstract
This is the first of a projected series of canonic reviews covering all invertebrate muscle literature prior to 2005 and covers muscle genes and proteins except those involved in excitation-contraction coupling (e.g., the ryanodine receptor) and those forming ligand- and voltage-dependent channels. Two themes are of primary importance. The first is the evolutionary antiquity of muscle proteins. Actin, myosin, and tropomyosin (at least, the presence of other muscle proteins in these organisms has not been examined) exist in muscle-like cells in Radiata, and almost all muscle proteins are present across Bilateria, implying that the first Bilaterian had a complete, or near-complete, complement of present-day muscle proteins. The second is the extraordinary diversity of protein isoforms and genetic mechanisms for producing them. This rich diversity suggests that studying invertebrate muscle proteins and genes can be usefully applied to resolve phylogenetic relationships and to understand protein assembly coevolution. Fully achieving these goals, however, will require examination of a much broader range of species than has been heretofore performed.
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Affiliation(s)
- Scott L Hooper
- Neuroscience Program, Department of Biological Sciences, Irvine Hall, Ohio University, Athens, Ohio 45701, USA.
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Intron variability in an actin gene can be used to discriminate between chicken and turkey DNA. Meat Sci 2002; 61:163-8. [DOI: 10.1016/s0309-1740(01)00180-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2001] [Accepted: 08/21/2001] [Indexed: 11/24/2022]
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Fernandez A, García T, Gonzalez I, Asensio L, Rodriguez MA, Hernández PE, Martin R. Polymerase chain reaction-restriction fragment length polymorphism analysis of a 16S rRNA gene fragment for authentication of four clam species. J Food Prot 2002; 65:692-5. [PMID: 11952222 DOI: 10.4315/0362-028x-65.4.692] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Specific identification of four clam species, Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), Ruditapes philippinarum (Japanese carpet shell), and Venerupis rhomboides (yellow carpet shell), was achieved by polymerase chain reaction-restriction fragment length polymorphism analysis of a fragment of the mitochondrial 16S rRNA gene. Amplification of DNA isolated from the foot muscle produced fragments of 511 bp for V. pullastra, 523 bp for R. decussatus, 545 bp for R. philippinarum, and 502 bp for V. rhomboides. The restriction profiles obtained by agarose gel electrophoresis when amplicons were digested with endonucleases BsmAI and BsrI allowed unequivocal identification of the four clam species. This approach would be less costly, simpler, and quicker than conventional sequencing of polymerase chain reaction products followed by detailed comparison of individual sequences, especially when large numbers of samples need to be analyzed.
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Affiliation(s)
- Alicia Fernandez
- Departamento de Nutrición y Bromatología III, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
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Rego I, Martínez A, González-Tizón A, Vieites J, Leira F, Méndez J. PCR technique for identification of mussel species. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2002; 50:1780-1784. [PMID: 11902912 DOI: 10.1021/jf0110957] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Random amplified polymorphic DNA (RAPD) analysis has been applied to the identification of four mussels species: Mytilus edulis, Mytilus chilensis, Mytilus galloprovincialis, and Perna canaliculus. Amplifications of DNA from mussel were carried out using random primers. The most distinctive bands were then isolated, cloned, and sequenced to design specific primers. Finally, DNA from different mussels was amplified with these specific primers, and results allow genetic identification of M. galloprovincialis from the rest of the mussel species.
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Affiliation(s)
- Ignacio Rego
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidade da Coruña, A Zapateira s/n, 15071 La Coruña, Spain
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