A polymerase chain reaction-restriction fragment length polymorphism method based on the analysis of a 16S rRNA/tRNAVal mitochondrial region for species identification of commercial penaeid shrimps (Crustacea: Decapoda: Penaeoidea) of food interest

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.

Molecular identification of biwa trout (Oncorhynchus masou rhodurus) using PCR-RFLP method

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was used to identify meat from biwa trout (Oncorhynchus masou rhodurus), amago trout (Oncorhynchus masou ishikawae), yamame trout (Oncorhynchus masou masou), and rainbow trout (Oncorhynchus mykiss). PCR amplification was conducted using primers flanking conserved regions of NADH dehydrogenase subunits 4 and 5 (ND4-ND5) (2848 bp) and ND1 (1091 bp) genes of mitochondrial DNA following restriction digestion with the enzyme HaeIII. Although the segments of ND4-ND5 and ND1 genes showed intraspecies variation, the generation of DNA fragments larger than 300 bp and 160 bp following cleavage by HaeIII of ND4-ND5 and ND1, respectively, was efficient to differentiate the four species. Furthermore, this method was successful in species identification even when using PCR-amplified products obtained from thermally processed biwa trout samples. This sensitive technique can be utilized to reveal commercial fraud, where biwa trout is adulterated with meat from cheaper counterparts.

Morphological identification and molecular confirmation of the deep-sea blue and red shrimp Aristeus antennatus larvae

The early life stages of the blue and red shrimp Aristeus antennatus (Decapoda: Dendrobranchiata: Penaeoidea: Aristeidae) were described by Heldt in 1955 based on plankton samples, larval rearing and assumptions of species habitat. Even with adequate keys, identification of its first larval stages remained a difficult task due to the lack of specific morphological characters which would differentiate them from other Penaeoidea species. Larvae of Aristeus antennatus were collected in the continental slope off the Spanish Mediterranean coast in August 2016 with a neuston net and preserved in ethanol 96%. DNA from the larvae was extracted and the molecular markers Cytochrome Oxidase I and 16S rDNA were sequenced and compared to that of adults with the objective of confirming the previous morphological description. Then, we present additional information to the morphological description of Aristeus antennatus larval stages through scanning electron microscopy and molecular analysis. This represents the first documented occurrence of Aristeus antennatus larvae off the Catalan coast and sets the grounds for further work on larval ecology and population connectivity of the species, which is an important contribution to a more sustainable fishery.

Identification of Peptide Biomarkers for Discrimination of Shrimp Species through SWATH-MS-Based Proteomics and Chemometrics

Incorrect labeling and adulteration of shrimp occurs due to interspecies similarities and carapace removal during processing. This study attempted to identify three related commercial shrimp species of the order Decapoda: Marsupenaeus japonicus, Fenneropenaeus chinensis, and Litopenaeus vannamei. All measurable trypsin-digested peptides in the individual shrimp were detected using ultrahigh-performance liquid chromatography quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition. Further analysis of peptide biomarkers was carried out with an orthogonal partial least-squares discriminant analysis (OPLS-DA) model. BLAST was used for species-specific analysis. Subsequently, multiple reaction monitoring (MRM) methods were developed for sensitivity and selectivity screening of the selected peptides, and 27 were identified as biomarkers allowing rapid and accurate discrimination of shrimp species without high-resolution mass spectrometry or statistical model building. These strategies could be applied in authentication of other products containing highly homologous proteomes.

A single enzyme PCR-RFLP protocol targeting 16S rRNA/tRNAval region to authenticate four commercially important shrimp species in India

Food authenticity is an issue of major concern for food authorities, as mislabeling represents one of the major commercial frauds. In this study, a novel PCR-RFLP protocol was developed as a tool to authenticate four shrimp products of commercial importance belonging to the family, Penaeidae, viz. Litopenaeus vannamei, Penaeus monodon, P. semisulcatus and Fenneropenaeus indicus. PCR amplification was performed targeting 16S rRNA/tRNA^val region having an amplicon size of 530bp using the specific primers for shrimps, 16S-Cru4/16S-Cru3. Subsequent restriction analysis with a single restriction enzyme, Tsp5091, yielded distinct RFLP pattern for each species of shrimps having fragment sizes below 150bp. The unique RFLP patterns were also obtained in processed shrimp products without any degradation or alteration in the major fragments. The method was also validated with commercial shrimp products. Thus, the developed protocol can be performed within 8h using a single enzyme to authenticate four shrimp products of commercial significance.

Tuna Species Substitution in the Spanish Commercial Chain: A Knock-On Effect

Intentional mislabelling of seafood is a widespread problem, particularly with high-value species like tuna. In this study we examine tuna mislabelling, deliberate species substitution, types of substitution and its impact on prices. The survey covered the commercial chain, from Merca-Barna to fishmongers and restaurants in the Spanish Autonomous Community of Catalonia. To understand the geographic extent of the problem we also sampled Merca-Madrid, Europe's biggest fish market, and Merca-Málaga for its proximity to the bluefin tuna migratory route and trap fishery. Monthly surveys were carried out over one year. The results showed a high deficiency in labelling: 75% of points of sale and 83% of restaurants did not specify the species, and in those cases the name of the species had to be asked. A total of 375 samples were analysed genetically, the largest dataset gathered in Europe so far. The identified species were Thunnus albacares, Thunnus thynnus and Thunnus obesus. Species substitution began at suppliers, with 40% of observed cases, increasing to 58% at fishmongers and 62% at restaurants. The substitution was mainly on bluefin tuna (T. thynnus), 73% of cases. At restaurants, only during the bluefin fishing season, we observed a decrease of Bluefin tuna substitution and an increase of reverse substitution revealing some illegal fishing. The effect of species substitution on species prices was relevant: T. obesus increased its price by around €12 kg-1 when it was sold as bluefin. In view of the deficiency of labelling, the abuse of generic names and the lack of the bluefin catch document, we conclude that the Spanish regulations are ineffective, highlighting the need for policy execution, and the urgent need for information campaigns to Spanish consumers.

Species identification through mitochondrial rRNA genetic analysis

Inter-species and intraspecific variations in mitochondrial DNA (mtDNA) were observed in a bioinformatics analysis of the mitochondrial genomic sequences of 11 animal species. Some highly conserved regions were identified in the mitochondrial 12S and 16S ribosomal RNA (rRNA) genes of these species. To test whether these sequences are universally conserved, primers were designed to target the conserved regions of these two genes and were used to amplify DNA from 21 animal tissues, including two of unknown origin. By sequencing these PCR amplicons and aligning the sequences to a database of non-redundant nucleotide sequences, it was confirmed that these amplicons aligned specifically to mtDNA sequences from the expected species of origin. This molecular technique, when combined with bioinformatics, provides a reliable method for the taxonomic classification of animal tissues.

Species identification of the Northern shrimp (Pandalus borealis) by polymerase chain reaction-restriction fragment length polymorphism and proteomic analysis

Genomic and proteomic techniques for species identification of meat and seafood products are being widely used. In this study, a genomic approach was used to differentiate Pandalus borealis (the Northern shrimp), which belongs to the superfamily Pandaloidea, from 30 crustaceans consisting of 19 commercially relevant prawns/shrimps species that belong to the superfamily Penaeoidea, which include the families Penaeidae and Solenoceridae, and 11 other crustacean species, including prawns, shrimps, lobsters, and crabs. For this purpose, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was designed based on the amplification of the 16S rRNA/tRNA(Val)/12S rRNA mitochondrial regions using the primers 16S-CruF and 16S-CruR. The 966-bp PCR products were produced and cleaved with the restriction enzymes AluI, TaqI, and HinfI, which provided species-specific restriction patterns. In addition, a proteomic approach, based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization-ion trap (ESI-IT) mass spectrometry, was used to identify and characterize new P. borealis-specific peptides that could be useful as potential markers of this species in protein-based detection methods. To our knowledge, this is the first time a molecular method has been successfully applied to identify a wide range of prawn and shrimp species, including P. borealis, for either whole individuals or processed products. However, validation of the methods proposed here is required by applying them to a larger sample of individuals from different populations and geographic origins in order to avoid mainly false-negative results.

Selected tandem mass spectrometry ion monitoring for the fast identification of seafood species

Selected tandem mass spectrometry (MS/MS) ion monitoring (SMIM) is the most suitable scanning mode to detect known peptides in complex samples when an ion-trap mass spectrometer is the instrument used for the analysis. In this mode, the MS detector is programmed to perform continuous MS/MS scans on one or more selected precursors, either during a selected time interval, or along the whole chromatographic run. MS/MS spectra are recorded, so virtual multiple reaction monitoring chromatogram traces for the different fragment ions can be plotted. In this work, a shotgun proteomics approach was applied to the detection of previously characterized species-specific peptides from different seafood species. The proposed methodology makes use of high intensity focused ultrasound-assisted trypsin digestion for ultra fast sample preparation, peptide separation and identification by reverse phase capillary LC coupled to an ion-trap working in the SMIM scanning mode. This methodology was applied to the differential classification of seven commercial, closely related, species of Decapoda shrimps proving to be an excellent tool for seafood product authentication, which may be used by fisheries and manufacturers to provide a fast and effective identification of the specimens, guaranteeing the quality and safety of foodstuffs to consumers.

Mass spectrometry characterization of species-specific peptides from arginine kinase for the identification of commercially relevant shrimp species

The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyses, is proposed for the identification of shrimp species with commercial interest. MALDI-TOF peptide mass fingerprint from arginine kinase tryptic digests were used for the identification of seven commercial, closely related species of Decapoda shrimps. Further identification and characterization of these peptides was performed by CID on an ESI-IT instrument, database search and de novo sequence interpretation, paying special attention to differential, species-specific peptides. Fisheries and manufacturers may take advantage of this methodology as a tool for a rapid and effective seafood product identification and authentication, providing and guaranteeing the quality and safety of the foodstuffs to consumers.

Arginine kinase peptide mass fingerprinting as a proteomic approach for species identification and taxonomic analysis of commercially relevant shrimp species

A proteomic approach aimed at species identification and taxonomic analysis of shrimp species of commercial interest is presented. Six different species belonging to the order Decapoda were considered. Preliminary, two-dimensional gel electrophoresis (2-DE) analysis of the sarcoplasmic proteome revealed interspecific variability in the isoelectric point (pI) of arginine kinase. For this reason, arginine kinase spot was selected as a potential molecular marker and subjected to tryptic digestion followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) peptide mass fingerprinting (PMF) analysis. Arginine kinase PMF allowed the differentiation of the six species studied. Four samples of commercial origin obtained in local markets were analyzed to validate the methodology. The PMF cluster analysis also provided information about the phylogenetic relationships in these species. The application of this methodology may be of interest for the differentiation and taxonomic analysis of shrimp species complementing DNA-based phylogenetic studies.