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

Hue-change coupled with CRISPR-Cas12a lateral flow assay for the semiquantitative detection of Salmo salar adulteration

Salmo salar is one of the most popular salmon species due to its meaty texture and quality protein. Oncorhynchus mykiss, which has a muscle texture similar to that of Salmo salar and is less expensive, is often used as a substitute for Salmo salar. As Salmo salar and Oncorhynchus mykiss belong to the same subfamily of Salmonidae, traditional methods are ineffective in the specific detection of the two. In this study, we combined hue-change with CRISPR/Cas12a lateral flow assay to detect the Salmo salar adulteration. This method detected S. salar genomic DNA at a vLOD of 5 copies, and was able to accurately identify adulterated samples containing 5 % w/w Salmo salar within one hour. In addition, the detection of Salmo salar in processed food products was achieved with the naked-eye at a concentration range of 0 % ∼ 70 % w/w, and the detection accuracy is between 93.3 % ∼ 100 %.

Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods

Next-generation sequencing and other sequencing approaches have made significant progress in DNA analysis. However, there are indispensable advantages in the nonsequencing methods. They have their justifications such as being speedy, cost-effective, multi-applicable, and straightforward. Among the nonsequencing methods, the genome profiling method is worthy of reviewing because of its high potential. This article first reviews its basic properties, highlights the key concept of species identification dots (spiddos), and then summarizes its various applications.

A Novel Method for Rapid Screening of Salmonidae Ingredients and Accurate Detection of Atlantic Salmon (Salmo salar) Simultaneously Using Duplex Real-Time PCR Coupled with Melting Curve Analysis

The substitution of ingredients with Salmonidae, particularly Salmo salar, has led to widespread reports of financial losses and health risks globally, emphasizing the urgent need for the development of a rapid and precise method for species identification. The aim of the present study was to develop a novel method for the rapid screening of Salmonidae ingredients and the accurate detection of S. salar simultaneously using multiplex real-time PCR coupled with melting curve analysis. Specifically, primer sets specific for S. salar and Salmonidae were cross-confirmed. Moreover, the reaction system and conditions of a real-time duplex PCR were optimized, and the proposed methodology was verified, proving that the assay has good specificity and sensitivity. Clear and distinguishable melting peaks, with expected Tm values of around 80 °C (S. salar) and 84 °C (Salmonidae), were observed for twelve products, proving the presence of S. salar. However, four products were not derived from S. salar, but they could have belonged to another species within the Salmonidae family due to the presence of only one specific melting peak at a Tm value of about 84 °C. Therefore, the novel assay in the present study allows for the fast and accurate screening of Salmonidae ingredients and the detection of S. salar simultaneously.

The expansion of invasive species to the East: new sites of the bullheads (genus Ameiurus Rafinesque 1820) in Ukraine with morphological and genetic identification

This study confirms the extended distribution of two invasive species of the genus Ameiurus in Ukraine. Specifically, A. melas is recorded for the first time in the Southern Buh basin and A. nebulosus has expanded further eastward within the Dnipro basin. Material collected in 2019 and 2022 was identified by morphological features and confirmed by molecular genetic analysis. The most reliable morphological characters for distinguishing these two species include anal-fin membrane pigmentation (light or black), gill raker count (fewer or more than 16), and serrations on the pectoral-fin spine (well-developed along the full length or small, absent near the tip). The analysis of the cytochrome oxidase subunit I barcoding marker identified all samples from the Dnipro Basin (Tnia and Velykyi Luh localities) as A. nebulosus, while all specimens from the Vinnytsia region within the Southern Buh basin (Sotskoho and Vyshenske lakes) were attributed to A. melas. The maximum-likelihood analysis revealed clearly separated clades with high bootstrap support (>75%), strongly supporting the presence of the two separate species. This study suggests the potential for further eastward expansion of both species within Ukraine: A. nebulosus in the northern direction and A. melas in the southern direction.

Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Labeo catla parent populations

BACKGROUND

Interspecific hybrids of rohu (Labeo rohita) and catla (Labeo catla) are common, especially in India due to constrained breeding. These hybrids must segregate from their wild parents as part of conservational strategies. This study intended to screen the hybrids from wild rohu and catla parents using both morphometric and molecular approaches.

METHODS & RESULTS

The carp samples were collected from Jharkhand and West Bengal, India. The correlation and regression analysis of morphometric features are considered superficial but could be protracted statistically by clustering analysis and further consolidated by nucleotide variations of one mitochondrial and one nuclear gene to differentiate hybrids from their parents. Out of 21 morphometric features, 6 were used for clustering analysis that exhibited discrete separation among rohu, catla, and their hybrids when the data points were plotted in a low-dimensional 2-D plane using the first 2 principal components. Out of 40 selected single nucleotide polymorphism (SNP) positions of the COX1 gene, hybrid showed 100% similarity with catla. Concerning SNP similarity of the 18S rRNA nuclear gene, the hybrid showed 100% similarity with rohu but not with catla; exhibiting its probable parental inheritance.

CONCLUSIONS

Along with morphometric analysis, the SNP comparison study together points towards strong evidence of interspecific hybridization between rohu and catla, as these hybrids share both morphological and molecular differences with either parent. However, this study will help screen the hybrids from their wild parents, as a strategy for conservational management.

An innovative molecular approach towards the cost-effective entomological authentication of honey

Honey authentication and traceability are crucial not only for economic purposes but also for ensuring safety. However, the widespread adoption of cutting-edge technologies in practical applications has been hampered by complex, time-consuming sample pre-treatment processes, the need for skilled personnel, and substantial associated expenses. This study aimed to develop a simple and cost-effective molecular technique to verify the entomological source of honey. By utilizing newly designed primers, we successfully amplified the mitochondrial 16S ribosomal RNA gene of honey bees from honey, confirming the high quality of the extracted DNA. Employing RFLP analysis with AseI endonuclease, species-specific restriction patterns were generated for honey derived from six closely related honey bees of the Apis genus. Remarkably, this method was proven equally effective in identifying heat-treated and aged honey by presenting the same RFLP profiles as raw honey. As far as we know, this is the initial research of the simultaneous differentiation of honey from closely related honey bee species using the restriction endonuclease AseI and mitochondrial 16S rRNA gene fragments. As a result, it holds tremendous potential as a standardized guideline for regulatory agencies to ascertain the insect origins of honey and achieve comprehensive traceability.

Immunological and molecular diagnostic techniques in fish health: present and future prospectus

Fish health management is critical to aquaculture and fisheries as it directly affects sustainability and productivity. Fish disease diagnosis has taken a massive stride because of advances in immunological and molecular diagnostic tools which provide a sensitive, quick, and accurate means of identifying diseases. This review presents an overview of the main molecular and immunological diagnostic methods for determining the health of fish. The immunological techniques help to diagnose different fish diseases by detecting specific antigens and antibodies. The application of immunological techniques to vaccine development is also examined in this review. The genetic identification of pathogens is made possible by molecular diagnostic techniques that enable the precise identification of bacterial, viral, and parasitic organisms in addition to evaluating host reactions and genetic variation associated with resistance to disease. The combination of molecular and immunological methods has resulted in the creation of novel techniques for thorough evaluation of fish health. These developments improve treatment measures, pathogen identification and provide new information about the variables affecting fish health, such as genetic predispositions and environmental stresses. In the framework of sustainable fish farming and fisheries management, this paper focuses on the importance of these diagnostic techniques that play a crucial role in protecting fish populations and the aquatic habitats. This review also examines the present and potential future directions in immunological and molecular diagnostic techniques in fish health.

Recent advancements with loop-mediated isothermal amplification (LAMP) in assessment of the species authenticity with meat and seafood products

Species adulteration or mislabeling with meat and seafood products could negatively affect the fair trade, wildlife conservation, food safety, religion aspect, and even the public health. While PCR-based methods remain the gold standard for assessment of the species authenticity, there is an urgent need for alternative testing platforms that are rapid, accurate, simple, and portable. Owing to its ease of use, low cost, and rapidity, LAMP is becoming increasingly used method in food analysis for detecting species adulteration or mislabeling. In this review, we outline how the features of LAMP have been leveraged for species authentication test with meat and seafood products. Meanwhile, as the trend of LAMP detection is simple, rapid and instrument-free, it is of great necessity to carry out end-point visual detection, and the principles of various end-point colorimetry methods are also reviewed. Moreover, with the aim to enhance the LAMP reaction, different strategies are summarized to either suppress the nonspecific amplification, or to avoid the results of nonspecific amplification. Finally, microfluidic chip is a promising point-of-care method, which has been the subject of a great deal of research directed toward the development of microfluidic platforms-based LAMP systems for the species authenticity with meat and seafood products.

Fish DNA Sensors for Authenticity Assessment-Application to Sardine Species Identification

Food and fish adulteration is a major public concern worldwide. Apart from economic fraud, health issues are in the forefront mainly due to severe allergies. Sardines are one of the most vulnerable-to-adulteration fish species due to their high nutritional value. Adulteration comprises the substitution of one fish species with similar species of lower nutritional value and lower cost. The detection of adulteration, especially in processed fish products, is very challenging because the morphological characteristics of the tissues change, making identification by the naked eye very difficult. Therefore, new analytical methods and (bio)sensors that provide fast analysis with high specificity, especially between closely related fish species, are in high demand. DNA-based methods are considered as important analytical tools for food adulteration detection. In this context, we report the first DNA sensors for sardine species identification. The sensing principle involves species recognition, via short hybridization of PCR-amplified sequences with specific probes, capture in the test zone of the sensor, and detection by the naked eye using gold nanoparticles as reporters; thus, avoiding the need for expensive instruments. As low as 5% adulteration of Sardina pilchardus with Sardinella aurita was detected with high reproducibility in the processed mixtures simulating canned fish products.

Visual and rapid detection of escolar (Lepidocybium flavobrunneum) using loop mediated isothermal amplification in conjunction with a specific molecular beacon probe

Species adulteration has become a main reason for the unexpected exposure to escolar, which is often related with the gastrointestinal disease called keriorrhea. Sensitive and accurate identification of escolar is required to protect consumers from commercial and health frauds. The present study established a visual and rapid method for escolar detection using LAMP (loop-mediated isothermal amplification) in conjunction with a MB (molecular beacon) probe. The visual MB-LAMP assay demonstrated high specificity and superb sensitivity (1 pg DNA) for escolar and low to 0.1 % (w/w) simulated adulteration could be detected within 25 min. Additionally, method validation on commercial products highlighted the umbrella term of white tuna for escolar on Chinese market. All these results indicated that the MB-LAMP method is a useful tool for rapid, sensitive and convenient detection of escolar and can also be used as a point-of-care molecular diagnostic technique since it does not require the expensive equipment.

Genetic Diversity in Natural Populations of the Near-Threatened Species Lignobrycon myersi (Characiformes, Triportheidae): Implications for Species Conservation

The river basins of Brazil contain a highly diverse ichthyofauna of remarkable endemism, including several threatened species. Accordingly, Lignobrycon myersi is a fish species distributed only in a few rivers from the state of Bahia, northeastern Brazil. Since this species is classified as Near Threatened and is poorly studied, efforts to understand the genetic structure of populations and putative cryptic forms should help define efficient strategies of management and conservation. Herein, the molecular identification and the population genetic diversity of specimens of L. myersi across their range (Almada, Contas, and Cachoeira river basins) were assessed using mitochondrial markers (16S rDNA and D-Loop, respectively). The inferences based on phylogenetics, genetic distance, and species delimitation methods invariably identified all samples as L. myersi. In addition, sequencing of D-loop fragments revealed significant haplotype diversity and a considerable level of population genetic structure. Despite their geographic isolation, these data suggested that populations from Almada and Contas rivers represent a single evolutionary lineage that could be managed as a whole. In contrast, the population from Cachoeira River was highly differentiated from the others and should be managed separately as a unique and endemic unit, particularly focused on the conservation of native habitats.

Current State of Milk, Dairy Products, Meat and Meat Products, Eggs, Fish and Fishery Products Authentication and Chemometrics

Food fraud is a matter of major concern as many foods and beverages do not follow their labelling. Because of economic interests, as well as consumers' health protection, the related topics, food adulteration, counterfeiting, substitution and inaccurate labelling, have become top issues and priorities in food safety and quality. In addition, globalized and complex food supply chains have increased rapidly and contribute to a growing problem affecting local, regional and global food systems. Animal origin food products such as milk, dairy products, meat and meat products, eggs and fish and fishery products are included in the most commonly adulterated food items. In order to prevent unfair competition and protect the rights of consumers, it is vital to detect any kind of adulteration to them. Geographical origin, production methods and farming systems, species identification, processing treatments and the detection of adulterants are among the important authenticity problems for these foods. The existence of accurate and automated analytical techniques in combination with available chemometric tools provides reliable information about adulteration and fraud. Therefore, the purpose of this review is to present the advances made through recent studies in terms of the analytical techniques and chemometric approaches that have been developed to address the authenticity issues in animal origin food products.

A Novel Machine-Learning Framework Based on a Hierarchy of Dispute Models for the Identification of Fish Species Using Multi-Mode Spectroscopy

Seafood mislabeling rates of approximately 20% have been reported globally. Traditional methods for fish species identification, such as DNA analysis and polymerase chain reaction (PCR), are expensive and time-consuming, and require skilled technicians and specialized equipment. The combination of spectroscopy and machine learning presents a promising approach to overcome these challenges. In our study, we took a comprehensive approach by considering a total of 43 different fish species and employing three modes of spectroscopy: fluorescence (Fluor), and reflectance in the visible near-infrared (VNIR) and short-wave near-infrared (SWIR). To achieve higher accuracies, we developed a novel machine-learning framework, where groups of similar fish types were identified and specialized classifiers were trained for each group. The incorporation of global (single artificial intelligence for all species) and dispute classification models created a hierarchical decision process, yielding higher performances. For Fluor, VNIR, and SWIR, accuracies increased from 80%, 75%, and 49% to 83%, 81%, and 58%, respectively. Furthermore, certain species witnessed remarkable performance enhancements of up to 40% in single-mode identification. The fusion of all three spectroscopic modes further boosted the performance of the best single mode, averaged over all species, by 9%. Fish species mislabeling not only poses health-related risks due to contaminants, toxins, and allergens that could be life-threatening, but also gives rise to economic and environmental hazards and loss of nutritional benefits. Our proposed method can detect fish fraud as a real-time alternative to DNA barcoding and other standard methods. The hierarchical system of dispute models proposed in this work is a novel machine-learning tool not limited to this application, and can improve accuracy in any classification problem which contains a large number of classes.

New perspective on mechanism in muscle toxicity of ochratoxin A: Model of juvenile grass carp (Ctenopharyngodon idella)

Ochratoxin A (OTA) is a common fungal toxin that pollutes raw materials of aquatic feeds (such as corn, soybean meal, and wheat). This study explored the effects of OTA through diet on muscle toxicity in juvenile grass carp (Ctenopharyngodon idella). The following results were obtained for the muscle. (1) With an increase in dietary OTA, the residue of OTA in muscle increased, muscle fiber diameter and density decreased, and even muscle fiber breakage. (2) OTA caused oxidative stress by downregulating GPx1 (a, b) and Trx via inhibited the PGC1-α/Nrf2 signaling pathway. (3) OTA exacerbated endoplasmic reticulum stress in the muscle by causing endoplasmic reticulum expansion (results of transmission electron microscopy) and upregulating the expression of GRP78, eIF2α, ATF6, PERK, and CHOP. (4) OTA reduced muscle fiber diameter by inhibiting protein synthesis (AKT, TOR, and S6K1) and promoting the mRNA expression of protein degradation-related genes (MURF1, MAFBX, and FoxO3a), as well as by reducing AKT and promoting the immunofluorescence expression of FoxO3. (5) OTA inhibits collagen deposition by downregulating TGF-β1, TGF-βR1, Smad2, Smad3, Smad4, CTGF, TIMP, PHD, and LOX mRNA expressions as well as the CTGF immunofluorescence expression. Moreover, based on the GSH and collagen content contents, the upper safe dose for OTA-induced toxicity was 963.6 and 1129.6 μg/kg diet, respectively. Using the example of OTA, our research has provided new insights that raise concerns about the quality of aquatic products by exploring muscle toxicity caused by mycotoxins.

Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics

The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.

Cuttlefish Species Authentication: Advancing Label Control through Near-Infrared Spectroscopy as Rapid, Eco-Friendly, and Robust Approach

Accurate species identification, especially in the fishery sector, is critical for ensuring food safety, consumer protection and to prevent economic losses. In this study, a total of 93 individual frozen-thawed cuttlefish samples from four different species (S. officinalis, S. bertheloti, S. aculeata, and Sepiella inermis) were collected from two wholesale fish plants in Chioggia, Italy. Species identification was carried out by inspection through morphological features using dichotomic keys and then through near-infrared spectroscopy (NIRS) measurements. The NIRS data were collected using a handled-portable spectrophotometer, and the spectral range scanned was from 900-1680 nm. The collected spectra were processed using principal component analysis for unsupervised analysis and a support vector machine for supervised analysis to evaluate the species identification capability. The results showed that NIRS classification had a high overall accuracy of 93% in identifying the cuttlefish species. This finding highlights the robustness and effectiveness of spectral analysis as a tool for species identification, even in complex spatial contexts. The findings emphasize the potential of NIRS as a valuable tool in the field of fishery product authentication, offering a rapid and eco-friendly approach to species identification in the post-processing stages.

High-Resolution Melting (HRM) Analysis for Rapid Molecular Identification of Sparidae Species in the Greek Fish Market

The red porgy (Pagrus pagrus) and the common dentex (Dentex dentex) are Sparidae species of high commercial value, traded in the Greek market. In some cases, fish species identification from Greek fisheries is difficult for the consumer due to the strong morphological similarities with their imported counterparts or closely related species such as Pagrus major, Pagrus caeroleustictus, Dentex gibbosus and Pagellus erythrinus, especially when specimens are frozen, filleted or cooked. Techniques based on DNA sequencing, such as COI barcoding, accurately identify species substitution incidents; however, they are time consuming and expensive. In this study, regions of mtDNA were analyzed with RFLPs, multiplex PCR and HRM in order to develop a rapid method for species identification within the Sparidae family. HRM analysis of a 113 bp region of cytb and/or a 156 bp region of 16s could discriminate raw or cooked samples of P. pagrus and D. dentex from the aforementioned closely related species and P. pagrus specimens sampled in the Mediterranean Sea when compared to those fished in the eastern Atlantic. HRM analysis exhibited high accuracy and repeatability, revealing incidents of mislabeling. Multiple samples can be analyzed within three hours, rendering this method a useful tool in fish fraud monitoring.