Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species

The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.

Chilean Salmon Sushi: Genetics Reveals Product Mislabeling and a Lack of Reliable Information at the Point of Sale

Species diagnosis is essential to assess the level of mislabeling or misnamed seafood products such as sushi. In Chile, sushi typically includes salmon as the main ingredient, but species used are rarely declared on the menu. In order to identify which species are included in the Chilean sushi market, we analyzed 84 individual sushi rolls sold as "salmon" from sushi outlets in ten cities across Chile. Using a polymerase chain reaction-restriction fragment length polymorphism protocol (PCR-RFLP), we identified mislabeled and misnamed products. Atlantic salmon was the most common salmonid fish used in sushi, followed by coho salmon, rainbow trout, and Chinook salmon. We found a total of 23% and 18% of the products were mislabeled and misnamed, respectively. In 64% of cases, the salesperson selling the product could not identify the species. We also identified the use of wild-captured Chinook salmon samples from a naturalized population. Our results provide a first indication regarding species composition in Chilean sushi, a quantification of mislabeling and the level of misinformation declared by sales people to consumers. Finally, considering that Chinook salmon likely originates from a non-licensed origin and that sushi is an uncooked product, proper identification in the food production chain may have important consequences for the health of consumers.

COMplementary Primer ASymmetric PCR (COMPAS-PCR) Applied to the Identification of Salmo salar, Salmo trutta and Their Hybrids

Avoiding complementarity between primers when designing a PCR assay constitutes a central rule strongly anchored in the mind of the molecular scientist. 3'-complementarity will extend the primers during PCR elongation using one another as template, consequently disabling further possible involvement in traditional target amplification. However, a 5'-complementarity will leave the primers unchanged during PCR cycles, albeit sequestered to one another, therefore also suppressing target amplification. We show that 5'-complementarity between primers may be exploited in a new PCR method called COMplementary-Primer-Asymmetric (COMPAS)-PCR, using asymmetric primer concentrations to achieve target PCR amplification. Moreover, such a design may paradoxically reduce spurious non-target amplification by actively sequestering the limiting primer. The general principles were demonstrated using 5S rDNA direct repeats as target sequences to design a species-specific assay for identifying Salmo salar and Salmo trutta using almost fully complementary primers overlapping the same target sequence. Specificity was enhanced by using 3'-penultimate point mutations and the assay was further developed to enable identification of S. salar x S. trutta hybrids by High Resolution Melt analysis in a 35 min one-tube assay. This small paradigm shift, using highly complementary primers for PCR, should help develop robust assays that previously would not be considered.

High level of mislabeling in Spanish and Greek hake markets suggests the fraudulent introduction of African species

DNA analysis of hake products commercialized in southern European (Spanish and Greek) market chains have demonstrated more than 30% mislabeling, on the basis of species substitution. Tails and fillets were more mislabeled than other products, such as slices and whole pieces. African species were substitute species for products labeled as American and European species, and we suggest it is a case of deliberate economically profitable mislabeling because real market prices of European and American hake products are higher than those of African in Spanish market chains. The presented results suggest fraud detection that disadvantages African producers. Government-mandated genetic surveys of commercial hakes and the use of subsequent statements of fair trade on labels of seafood products could help to reduce fraud levels in a global market of increasingly conscious consumers sensitive to ethical issues.

Molecular organization of 5S rDNA in sharks of the genus Rhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes

In this study, we attempted a molecular characterization of the 5S rDNA in two closely related species of carcharhiniform sharks, Rhizoprionodon lalandii and Rhizoprionodon porosus, as well as a further comparative analysis of available data on lampreys, several fish groups and other vertebrates. Our data show that Rhizoprionodon sharks carry two 5S rDNA classes in their genomes: a short repeat class (termed class I) composed of approximately 185 bp repeats, and a large repeat class (termed class II) arrayed in approximately 465 bp units. These classes were differentiated by several base substitutions in the 5S coding region and by completely distinct non-transcribed spacers (NTS). In class II, both species showed a similar composition for both the gene coding region and the NTS region. In contrast, class I varied extensively both within and between the two shark species. A comparative analysis of 5S rRNA gene sequences of elasmobranchs and other vertebrates showed that class I is closely related to the bony fishes, whereas the class II gene formed a separate cartilaginous clade. The presence of two variant classes of 5S rDNA in sharks likely maintains the tendency for dual ribosomal classes observed in other fish species. The present data regarding the 5S rDNA organization provide insights into the dynamics and evolution of this multigene family in the fish genome, and they may also be useful in clarifying aspects of vertebrate genome evolution.

Detection of mislabeling in hake seafood employing mtSNPs-based methodology with identification of eleven hake species of the genus Merluccius

Species-specific DNA-based tags are valuable tools for the management of both fisheries and commercial fish products. Eleven hake species of the genus Merluccius have been identified employing mtSNPs-based methodology. The method is highly reproducible, fast, and technically easy. It is a reliable tool, allowing for routine analysis of commercial seafood. It can be applied by nonexperts in genetics because both laboratory handling and interpretation of results are easy and direct. The convenience of routine surveys in fish markets has been clearly established with a survey of commercial hake batches imported in south Europe. A total of 40 commercial processed hake were analyzed in this study. More than 20% of mislabeling has been detected.

DNA-Based Methods for the Identification of Commercial Fish and Seafood Species

  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.

Tetrodotoxin Poisoning

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.

5S rDNA variation and its phylogenetic inference in the genus Leporinus (Characiformes: Anostomidae)

5S rDNA sequences have proven to be valuable as genetic markers to distinguish closely related species and also in the understanding of the dynamic of repetitive sequences in the genomes. In the aim to contribute to the knowledge of the evolutionary history of Leporinus (Anostomidae) and also to contribute to the understanding of the 5S rDNA sequences organization in the fish genome, analyses of 5S rDNA sequences were conducted in seven species of this genus. The 5S rRNA gene sequence was highly conserved among Leporinus species, whereas NTS exhibit high levels of variations related to insertions, deletions, microrepeats, and base substitutions. The phylogenetic analysis of the 5S rDNA sequences clustered the species into two clades that are in agreement with cytogenetic and morphological data.

Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes

Some units of the 5S rDNA of Solea senegalensis were amplified by PCR and sequenced. Three main PCR products (227, 441, and 2166 bp) were identified. The 227- and 441-bp fragments were characterized by highly divergent nontranscribed spacer sequences (referred to as NTS-I and NTS-II) that were 109 and 324 bp long, respectively, yet their coding sequences were nearly identical. The 2166-bp 5S rDNA unit was composed of two 5S rRNA genes separated by NTS-I and followed by a 1721-bp spacer containing the U2, U5, and U1 small nuclear RNA genes (snRNAs). They were inverted and arranged in the transcriptional direction opposite that of the 5S rRNA gene. This simultaneous linkage of 3 different snRNAs had never been observed before. The PCR products were used as probes in fluorescence in situ hybridization experiments to locate the corresponding loci on the chromosomes of S. senegalensis. A major 5S rDNA chromosomal site was located along most of the short arm of a submetacentric pair, while a minor site was detected near the centromeric region of an acrocentric pair.

Identification of highly prized commercial fish using a PCR-based methodology

We report a practical class designed for undergraduate students of Marine Sciences as a part of the Genetics course. The class can also be included in undergraduate studies of food technology. The exercise was designed to emphasize the application of molecular biology techniques to fish species authentication and traceability. After a simple and rapid protocol for DNA extraction, PCR was used to analyze variation in size of individual 5S ribosomal gene spacer sequences in eight commercially important fishes. The resulting fragments containing these sequences were separated on agarose gels and visualized under a UV lamp. Differences in fragment length can be used to differentiate between species. This method is particularly useful in the identification of larvae, eggs, and processed food including frozen and canned products.

Novel method for the authentication of frigate tunas (Auxis thazard and Auxis rochei) in commercial canned products

A novel procedure for the authentication of frigate tunas (Auxis thazard and Auxis rochei) in commercially canned products has been developed. Three mitochondrial regions were simultaneously amplified by multiplex-Polymerase Chain Reaction, one corresponding to the small rRNA 12S subunit as a positive amplification control and two species-specific fragments corresponding to cytochrome b for A. rochei and ATPase 6 for A. thazard, respectively. Testing of two different detection systems revealed the fluorescence-based approach as the most sensitive. The results demonstrate that this rapid, low-cost methodology is a reliable molecular tool for direct application in the authentication of canned products.

Genetic identification of nine hake species for detection of commercial fraud

This study describes the 5S rRNA gene as a simple and reliable one-step PCR-based genetic marker that allows unambiguous identification of Merluccius paradoxus, Merluccius senegalensis, Merluccius australis, Merluccius gayi, Merluccius bilinearis, Merluccius hubbsi, and Macruronus magellanicus. The marker is based on differences in length at the nontranscribed spacer within the 5S rRNA genes and is robust enough for identification of processed products, such as fish fingers and other precooked commercial hake. Further restriction fragment length polymorphism analysis at the mitochondrial cytochrome b gene can distinguish Merluccius merluccius and Merluccius capensis. The application of these markers for routine works such as surveys of quality and labeling of commercial hakes is suggested due to their accuracy, low price, and possible automation for large-scale surveys.

Identification of Atlantic hake species by a simple PCR-based methodology employing microsatellite loci

Three Atlantic hake species (Merluccius merluccius, M. bilinearis, and M. hubbsi) were PCR typed for two microsatellite loci. A blind survey of the markers in samples of the three species determined the suitability of microsatellite loci for identification of hake product. All the analyzed samples were correctly assigned to the corresponding species. Typing of processed products (fish fingers, preprocessed frozen pieces) employing an automated sequencer was successful. This simple (PCR + fragment size) automated determination method is faster than any other method yet described for identification of hake commercial products.

Development of a specific monoclonal antibody for grouper (Epinephelus guaza) identification by an indirect enzyme-linked immunosorbent assay

Identification of fish species adulteration is important for consumer protection and the enforcement of food-labeling laws. A monoclonal antibody (MAb) generated against soluble muscle proteins from grouper (Epinephelus guaza) has been used in two indirect enzyme-linked immunosorbent assay (ELISA) formats (microtiter plates and immunostick tubes) for the rapid authentication of grouper fillets. The 3D12 MAb was produced with the use of the hybridoma technique and tested against several commonly consumed fish species by ELISA. The 3D12 MAb specifically reacted with grouper samples and could be useful for the discrimination of grouper among other, less-valued, fish species sold in the marketplace.

PCR technique for identification of mussel species

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.

Identification of goose (Anser anser) and mule duck (Anasplatyrhynchos x Cairina moschata) foie gras by multiplex polymerase chain reaction amplification of the 5S RDNA gene

Polymerase chain reaction (PCR) amplification of the nuclear 5S rDNA gene has been used for the identification of goose and mule duck foie gras. Two species-specific reverse primers were designed and used in a multiplex reaction, together with a forward universal primer, to amplify specific fragments of the 5S rDNA in each species. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear identification of goose and mule duck foie gras samples. This genetic marker can be useful for detecting fraudulent substitution of the duck liver for the more expensive goose liver.