Universal mitochondrial 16s rRNA biomarker for mini-barcode to identify fish species in Malaysian fish products

A review of CRISPR-Cas and PCR-based methods for the detection of animal species in the food chain-current challenges and future prospects

Regular testing and systematic investigation play a vital role to ensure product safety. Until now, the existing food authentication techniques have been based on proteins, lipids, and nucleic acid-based assays. Among various deoxyribonucleic acid (DNA)-based methods, the recently developed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based bio-sensing is an innovative and fast-expanding technology. The CRISPR/Cas-9 is known as Clustered Regularly Interspaced Short Palindromic Repeats due to the flexibility and simplicity of the CRISPR/Cas9 site-specific editing tool has been applied in many biological research areas such as Gene therapy, cell line development, discovering mechanisms of disease, and drug discovery. Nowadays, the CRISPR-Cas system has also been introduced into food authentication via detecting DNA barcodes of poultry and livestock both in processed and unprocessed food samples. This review documents various DNA based approaches, in an accessible format. Future CRISPR technologies are forecast while challenges are outlined.

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.

DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh

This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.

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.

Pragmatic applications of DNA barcoding markers in identification of fish species – a review

DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.

Molecular detection of spotted fever group rickettsiae in hedgehogs (Erinaceus amurensis) and hedgehog-attached ticks in Xuyi County, Southeast China

Tick-borne diseases like Rickettsia, Anaplasma and Ehrlichia are widespread infectious zoonoses that threaten the health of both humans and animals worldwide. Ticks and their hosts, such as hedgehogs, can play a crucial role in transmitting tick-borne diseases and the cycle of Rickettsia. To investigate the presence and identity of Rickettsia in hedgehogs and hedgehog-attached ticks in Xuyi County, Southeast China, 114 ticks were collected from 45 hedgehogs captured totally. Via morphological and molecular methods, all these ticks were identified as two species: Haemaphysalis flava (110/114, 96.5%) and Haemaphysalis longicornis (4/114, 3.5%). Rickettsia spp. were genotypically characterized by PCR targeting rrs, gltA, ompA, ompB, and sca4 gene fragments. The prevalence of spotted fever group rickettsiae (SFGR) infection found in hedgehogs and ticks was 17.8% (8/45) and 78.1% (89/114), respectively. Phylogenetic analyses demonstrated that those Rickettsia spp. belong to two species: Rickettsia heilongjiangensis (R. heilongjiangensis XY-1) and a potential new species, Candidatus Rickettsia xuyiensis XY-2. The present study gave the first evidence of R. heilongjiangensis and Candidatus R. xuyiensis in ticks and hedgehogs of Southeast China. Our findings suggest that hedgehogs might be involved in the natural transmission cycle of Rickettsia species.

DNA Barcode Identification of Fish Products from Guiyang Markets in Southwestern People's Republic of China

ABSTRACT

Global fish consumption is increasing in tandem with population growth, resulting in the dilemma of overfishing. Overfished high-value fish are often replaced with other fish in markets. Therefore, the accurate identification of fish products in the market is important. In this study, full-DNA and mini-DNA barcoding were used to detect fish product fraud in Guiyang, Guizhou Province, People's Republic of China. The molecular results revealed that 39 (20.42%) of the 191 samples were inconsistent with the labels. The percentages of mislabeling of fresh, frozen, cooked, and canned fish products were 11.70, 20.00, 34.09, and 50.00%, respectively. The average Kimura two-parameter distances of mini-DNA barcoding within species and within genera were 0.56 and 6.42%, respectively, and those of full-DNA barcoding were 0.53 and 7.25%, respectively. Commercial fraud was evident in this study; most high-priced fish were replaced with low-priced fish with similar features. Our findings indicate that DNA barcoding is an effective tool for identifying fish products and could be used to enhance transparency and fair trade in domestic fisheries.

HIGHLIGHTS

DNA barcoding of brackish and marine water fishes and shellfishes of Sundarbans, the world's largest mangrove ecosystem

The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish, aquatic molluscs and crustaceans of Sundarbans mangrove wetland, to build a reference library of fish and shellfishes of this unique ecosystems. A total of 185 mitochondrial COI barcode sequences and 59 partial sequences of the 16S rRNA gene were obtained from 120 genera, 65 families and 21 orders of fish, crustaceans and molluscs. The collected samples were first identified by examining morphometric characteristics and then assessed by DNA barcoding. The COI and 16S rRNA sequences of fishes and crustaceans were clearly discriminated among genera in their phylogenies. The average Kimura two-parameter (K2P) distances of COI barcode sequences within species, genera, and families of fishes are 1.57±0.06%, 15.16±0.23%, and 17.79±0.02%, respectively, and for 16S rRNA sequences, these values are 1.74±.8%, 0.97±.8%, and 4.29±1.3%, respectively. The minimum and maximum K2P distance based divergences in COI sequences of fishes are 0.19% and 36.27%, respectively. In crustaceans, the K2P distances within genera, families, and orders are 1.4±0.03%, 17.73±0.15%, and 22.81±0.02%, respectively and the minimum and maximum divergences are 0.2% and 33.93%, respectively. Additionally, the present study resolves the misidentification of the mud crab species of the Sundarbans as Scylla olivacea which was previously stated as Scylla serrata. In case of molluscs, values of interspecific divergence ranges from 17.43% to 66.3% in the barcoded species. The present study describes the development of a molecular and morphometric cross-referenced inventory of fish and shellfish of the Sundarbans. This inventory will be useful in future biodiversity studies and in forming future conservation plan.

Short targeting multiplex PCR assay to detect and discriminate beef, buffalo, chicken, duck, goat, sheep and pork DNA in food products

Food fraud is a global problem raising increased concerns during the past decades and food authenticity is now a burning issue. Beef, buffalo, chicken, duck, goat, sheep, and pork are heavily consumed meats bearing nutritional, economic and cultural/religious importance and are often found to be adulterated in raw and processed states. To authenticate these species, we developed and validated a highly specific multiplex (heptaplex) PCR assay targeting short length amplicons (73-263 bp) using seven pairs of species-specific primer sets targeting mitochondrial cytochrome b (cytb) and NADH dehydrogenase subunit 5 (ND5) genes. Specificity checking (in silico and in vitro) against 25 non-target species revealed no cross-species amplification. The developed multiplex assay was validated with various adulterated and heat-treated (boiled, microwaved and autoclaved) meatball products and were found to show high sensitivity and stability under all processing conditions. The assay was sensitive enough to detect 0.01-0.005 ng of DNA from raw meat and 0.5% (w/w) adulterated meat in mixed matrices. A market survey revealed mislabelling of 95% beef and 15% chicken products while pork products were found pure. Given some advantageous features including short sizes of amplicons, exceptional stability and superior sensitivity, the developed assay could be conveniently used for discriminatory detection of target species with a variety of raw meat as well as processed meat products undergoing extreme processing treatments.

DNA barcoding reveals fraud in commercial common snook (Centropomus undecimalis) products in Santa Marta, Colombia

The common snook Centropomus undecimalis is one of the main commercial fish species in the Caribbean region, including Colombia, where its populations have drastically decreased due to overfishing and environmental degradation. Thus, there is a market imbalance between the availability of snook products and their demand by consumers, which creates an opening for fraudulent actions such as species substitutions. Legislation in Colombia (and most Caribbean countries) lacks effective tools for the easy and rapid detection of frauds. Furthermore, there are very few studies published in scientific journals addressing this issue, of which none include C. undecimalis as the target species. Therefore, in order to investigate the existence of mislabeling in common snook products in Santa Marta, the present study analysed 44 frozen snook fillets from the five commercial brands available in the city. Moreover, 15 fresh snook fillets from six of the main fish markets were also analysed. To discover the frequency of possible frauds in labeling, samplings were carried out in July, September and November of 2019. Sample analyses involved the identification of each fillet at species level through molecular barcodes (16S-rRNA and COI), whose sequences were verified using BLAST and BOLD, and corroborated by a phylogenetic analysis. As a result, an astonishing 98% of the supermarkets fillets were found to be fraudulent, contrasting with a single case registered in the fish shop samples. The species used to substitute snook include the Pacific bearded brotula Brotula clarkae (38 samples), the Nile perch Lates niloticus (4 samples) and the acoupa weakfish Cynoscion acoupa (1 sample). Based on these results, there is a high rate of fraudulent labeling in the marketing of common snook in the city of Santa Marta, which calls for urgent actions to be taken by the corresponding authorities.

A rapid insect species identification system using mini-barcode pyrosequencing

BACKGROUND

Rapid and accurate species identification is not only important for biodiversity studies and pest quarantine and management, but in some cases may also influence the results of international trade negotiations. In this study, we developed a rapid species identification system for insects.

RESULTS

A universal DNA mini-barcode primer pair was designed to target ∼ 120 bp of the mitochondrial 16S rDNA gene. This primer set can amplify the targeted region from all 300 species of 26 insect orders tested as well as other classes of Arthropoda. Although we found no within-species variation in this region, it provided enough information to separate closely related species or species complexes, in particular Thrips spp. and Bemisia spp. By combining a quick DNA extraction method with pyrosequencing, we were able to generate DNA sequences and complete species identification within 5 h.

CONCLUSION

Mini-barcode pyrosequencing of 16S rDNA coupled with the GenBank database provides a rapid, accurate, and efficient species identification system. This system is therefore useful for biodiversity discovery, forensic identification, and quarantine control and management. © 2019 Society of Chemical Industry.

DNA barcoding reveals incorrect labelling of insects sold as food in the UK

Background

Insects form an established part of the diet in many parts of the world and insect food products are emerging into the European and North American marketplaces. Consumer confidence in product is key in developing this market, and accurate labelling of content identity is an important component of this. We used DNA barcoding to assess the accuracy of insect food products sold in the UK.

Methods

We purchased insects sold for human consumption from online retailers in the UK and compared the identity of the material ascertained from DNA barcoding to that stated on the product packaging. To this end, the COI sequence of mitochondrial DNA was amplified and sequenced, and compared the sequences produced to reference sequences in NCBI and the Barcode of Life Data System (BOLD).

Results

The barcode identity of all insects that were farmed was consistent with the packaging label. In contrast, disparity between barcode identity and package contents was revealed in two cases of foraged material (mopane worm and winged termites). One case of very broad family-level description was also highlighted, where material described as grasshopper was identified as Locusta migratoria from DNA barcode.

Conclusion

Overall these data indicate the need to establish tight protocols to validate product identity in this developing market. Maintaining biosafety and consumer confidence rely on accurate and consistent product labelling that provides a clear chain of information from producer to consumer.

Heptaplex Polymerase Chain Reaction Assay for the Simultaneous Detection of Beef, Buffalo, Chicken, Cat, Dog, Pork, and Fish in Raw and Heat-Treated Food Products

Species authentication of meat and fish products is crucial to safeguard public health, economic investment, and religious sanctity. We developed a heptaplex polymerase chain reaction assay targeting short amplicon length (73-198 bp) for the simultaneous detection and differentiation of cow, buffalo, chicken, cat, dog, pig, and fish species in raw and processed food using species-specific primers targeting mitochondrial cytb, ND5, and 16s rRNA genes. Assay validation of adulterated and various heat-treated meatball matrices showed excellent stability and sensitivity under all processing conditions. The detection limit was 0.01-0.001 ng of DNA under pure states and 0.5% meat in meatball products. Buffalo was detected in 86.7% (13 out of 15) of tested commercial beef products, while chicken, pork, and fish products were found to be pure. The developed assay was efficient enough to detect target species simultaneously, even in highly degraded and processed food products at reduced time.