Development of Multiplex PCR and Melt–Curve Analysis for the Molecular Identification of Four Species of the Mullidae Family, Available in the Market

Abstract

The authentication of food products and the verification of their identity are of major importance for consumers. Food fraud through mislabeling is an illegal practice consisting of the substitution of an expensive food product by a relatively cheaper one, misleading false labelling of their origin and adulteration in processed or frozen products. This issue is particularly of high importance concerning fish and seafood, which are easily adulterated primarily due to difficult morphological identification. Fish species of the Mullidae family are considered among the most high-valued seafood products traded in Greece and Eastern Mediterranean in general, in terms of the price and demand. Specifically, the red mullet (Mullus barbatus) and the striped red mullet (Mullus surmuletus) are both indigenous in the Aegean (FAO Division 37.3.1) and the Ionian (FAO Division 37.2.2) Seas, with high levels of consumers’ preferences. However, they could be easily adulterated or misidentified by the invasive Aegean Sea Lessepsian migrator goldband goatfish (Upeneus moluccensis) as well as by the imported West African goatfish (Pseudupeneus prayensis). Keeping this in mind, we designed two novel, time-saving and easy-to-apply multiplex PCR assays and one multiple Melt–Curve analysis real-time PCR for the identification of these four species. These methodologies are based on species-specific primers targeting single nucleotide polymorphisms (SNPs) detected via sequencing analysis of the mitochondrial cytochrome C oxidase subunit I (CO1) and of the cytochrome b (CYTB) genes in newly collected individuals, with additional comparison with congeneric and conspecific haplotypes obtained from the GenBank database. Both methodologies, targeting CO1 or CYTB, utilize one common and four diagnostic primers, producing amplicons of different length that are easily and reliably separated on agarose gel electrophoresis, yielding a single clear band of diagnostic size for each species or a certain Melt–Curve profile. The applicability of this cost-effective and fast methodology was tested in 328 collected specimens, including 10 cooked samples obtained from restaurants. In the vast majority (327 out of the 328) of the specimens tested, one single band was produced, in agreement with the expected products with a single exception a M. barbatus sample that was identified as M. surmuletus, the identity of which was confirmed using sequencing, indicating erroneous morphological identification. The developed methodologies are expected to contribute to the detection of commercial fraud in fish authentication.

Cytochrome b Sequencing as a Tool for Identification of Morphologically Similar Mediterranean Gobies Gobius incognitus and Gobius bucchichi (Actinopterygii: Gobiidae)

“…A high divergence in cyt b between G. incognitus and G. bucchichi, including numerous sites with fixed mutations (79 in total), enables clear distinctions between the two goby species at the mtDNA level. This relatively fast and low-cost method complements an array of molecular methods, such as multiplex PCR assays, melt curve analysis real-time PCR, or restriction fragment length polymorphism, which are successfully used for fish identification [73]. Importantly, molecular tools could also aid potential conservation efforts of less common species, for example, in this particular case, of G. bucchichi.…”

Rapid and Simultaneous Authentication of Six Laver Species Using Capillary Electrophoresis-Based Multiplex PCR

“…Recently, Giantsis et al (2023) presented a multiplex PCR for identifying fish species of the Mullidae family using mitochondrial genes with target lengths ranging from 106 to 438 bp [31]. Similarly, Saetang and Benjakul (2022) proposed a cytochrome b sequencebased PCR for detecting Asian seabass and mangrove red snapper with amplicon lengths between 268 and 480 bp [32].…”