DNA-based techniques for seafood species authentication

Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

BACKGROUND

Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae).

RESULTS

Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome C Oxidase subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit.

CONCLUSIONS

Target enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable subsequent studies in population genetics and adaptation of Latin American fish species and serve as a vital resource for conservation and management programs that rely on molecular data for species and genus-level identification.

A Droplet Digital PCR-Based Approach for Quantitative Analysis of the Adulteration of Atlantic Salmon with Rainbow Trout

Low-cost fish species are often used to adulterate or substitute for Atlantic salmon products, posing a serious threat to market order and public health. Hence, reliable techniques are urgently needed to detect Atlantic salmon adulteration. In this study, a precise method for identifying and quantifying adulterated Atlantic salmon with rainbow trout based on droplet digital PCR (ddPCR) testing was developed. Species-specific primers and probes were designed targeting the single-copy nuclear gene myoglobin of two salmonids. A quantitative formula for calculating the mass fraction of adulterated Atlantic salmon with rainbow trout was established based on a one-step conversion strategy, in which the DNA copy number ratios were directly transformed to meat mass fractions by introducing a fixed constant (the transfer coefficient). The dynamic range of the established ddPCR method was from 1% to 90%, with a limit of detection (LOD) of 0.2% and a limit of quantification (LOQ) of 0.8% for rainbow trout in Atlantic salmon, respectively. The quantification method demonstrated an acceptable level of repeatability and reproducibility, as the values of the relative standard deviation (RSD) for the tested meat mixtures with the known fractions were all less than 5%. Thermal and freezing treatments, as well as adding food additives within the recommended dosage limits, had no significant effect on the quantification accuracy. The method was successfully applied to detect rainbow trout adulteration in commercial raw and processed Atlantic salmon products. In comparison to real-time quantitative PCR (qPCR) testing, the established ddPCR method exhibited a higher level of stability and accuracy. Overall, the ddPCR-based quantitative method exhibited high levels of accuracy, stability, sensitivity, and practicability, suitable for applications in the routine surveillance and quality assurance of salmon products.

Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.

An Authentication Survey on Retail Seafood Products Sold on the Bulgarian Market Underlines the Need for Upgrading the Traceability System

Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three-year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods-MC; gastropods-MG; bivalves-MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA-based methods as tools for seafood authentication. The presence of non-compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level.

Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art

Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.

A Fast and Simple DNA Mini-barcoding and RPA Assay Coupled with Lateral Flow Assay for Fresh and Canned Mackerel Authentication

Nowadays, food authentication is more and more required given its relevance in terms of quality and safety. The seafood market is heavily affected by mislabelling and fraudulent substitutions/adulterations, especially for processed food products such as canned food items, due to the loss of morphological features. This study aims to develop new assays based on DNA to identify fresh mackerel (Scomber spp.) and commercial products. A new primer pair was de novo designed on the 5S rRNA gene and non-transcribed spacer (NTS), identifying a DNA mini-barcoding region suitable for species identification of processed commercial products. Moreover, to offer a fast and low-cost analysis, a new assay based on recombinase polymerase amplification (RPA) was developed for the identification of fresh 'Sgombro' (Scomber scombrus) and 'Lanzardo o Occhione' (Scomber japonicus and Scomber colias), coupled with the lateral flow visualisation for the most expensive species (Scomber scombrus) identification. This innovative portable assay has great potential for supply chain traceability in the seafood market.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12161-022-02429-6.

Innovation to limit seafood fraud post-COVID-19

Seafood is an important source of protein and micronutrients, but fishery stocks are increasingly under pressure from both legitimate and illegitimate fishing practices. Sustainable management of our oceans is a global responsibility, aligning with United Nations Sustainable Development Goal 14, Life Below Water. In a post-COVID-19 world, there is an opportunity to build back better, where locally sourced food via transparent supply chains are ever-more important. This article summarises emerging research of two innovative case studies in detecting and validating seafood provenance; and using alternative supply chains to minimise the opportunity for seafood fraud in a post-COVID-19 world.

Study on the physicochemical indexes, nutritional quality, and flavor compounds of Trichiurus lepturus from three representative origins for geographical traceability

Trichiurus lepturus (hairtail) is an important economic component of China's marine fishing industry. However, due to the difficulty in identifying the appearance of hairtail from different geographical distributions, hairtails with geographical indication trademarks were imitated by general varieties. In this study, the texture characteristics, color, basic nutrients, amino acids, mineral, fatty acids, and volatile flavor substances were used as indicators for multivariate statistical analysis to determine whether three origins of hairtails from the habitats of Zhoushan (East China Sea, T.Z), Hainan (South China Sea, T.N), and Qingdao (Yellow Sea, T.Q) in the market could be distinguished. The findings revealed that there were significant differences in amino acids composition, mineral composition, fatty acid composition in lipids, and volatile flavor substances among the hairtails of three origins (P < 0.05), but no differences in color, texture, protein content. T.Z had moisture, crude fat, essential amino acids (EAA), flavor amino acids (FAA), unsaturated fatty acids (UFA), and docosahexaenoic acids and dicosapentaenoic acids (ΣEPA + DHA) contents of 74.33, 5.4%, 58.25 mg⋅g-1, 46.20 mg⋅g-1, 66.84 and 19.38%, respectively, and the contents of volatile alcohols, aldehydes and ketones were 7.44, 5.30, and 5.38%, respectively. T.N contains moisture, crude fat, EAA, FAA, UFA and ΣEPA + DHA as 77.69, 2.38%, 64.76 mg⋅g-1, 52.44 mg⋅g-1, 65.52 and 29.45%, respectively, and the contents of volatile alcohols, aldehydes and ketones as 3.21, 8.92, and 10.98%, respectively. T.Q had the contents of moisture, crude fat, EAA, FAA, UFA, and ΣEPA + DHA 79.69, 1.43%, 60.9 mg⋅g-1, and 49.42 mg⋅g-1, respectively. The contents of unsaturated fatty acid and ΣEPA + DHA were 63.75 and 26.12%, respectively, while the volatile alcohols, aldehydes, and ketones were 5.14, 5.99, and 7.85%, respectively. Partial least squares-discriminant analysis (PLS-DA) multivariate statistical analysis showed that volatile flavor compounds could be used as the most ideal indicators for tracing the source of hairtail. In conclusion, the findings of this study can distinguish the three hairtail origins using some basic indicators, providing ideas for hairtail geographical identification.

Development of loop-mediated isothermal amplification (LAMP) assay for rapid and direct screening of yellowfin tuna (Thunnus albacares) in commercial fish products

Tuna is one of the most widely consumed fish on the European market, being available in various consumable options. Among them, Thunnus albacares, also called yellowfin tuna, is a delicacy and is consumed by millions of people around the world. Due to its comparatively high cost and demand, it is more vulnerable to fraud, where low-cost tuna or other fish varieties might be replaced for economic gain. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed and validated for targeting the mitochondrial cytochrome b gene for fast and direct detection of Thunnus albacares, which is a valuable tuna species. The analytical specificity was confirmed using 18 target samples (Thunnus albacares) and 18 samples of non-target fish species. The analytical sensitivity of the LAMP assay was 540 fg DNA per reaction. In addition, a simple and direct swab method without time-consuming nucleic acid extraction procedures and the necessity for cost-intensive laboratory equipment was performed that allowed LAMP detection of Thunnus albacares samples within 13 minutes. Due to its high specificity and sensitivity, the LAMP assay can be used as a rapid and on-site screening method for identifying Thunnus albacares, potentially providing a valuable monitoring tool for food authenticity control by the authorities.

Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing

DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.