Melt-curve-multiplex-haplotype-specific-PCR, a valuable tool for biological studies: Application in congeneric species discrimination assay

Georgiadis, Andreas; Sandaltzopoulos, Raphael; Stergiou, Kostas I.; Apostolidis, Apostolos P.

doi:10.1016/j.bse.2014.07.013

Cited by 3 publications

(6 citation statements)

References 22 publications

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“…On the other hand, although Turan (2011) previously reported no genetic distance among S. maena and S. smaris, the existence of a 4.44% genetic distance based on the mitochondrial DNA 16S rRNA gene sequences was determined with this study. Similarly, the phylogenetic tree topologies obtained from the mitochondrial cyt b and 16S rRNA gene sequence analyses (Figure 3, 4) also supported a closer genetic relationship between S. flexuosa and S. maena than to S. smaris, confirming the results reported by previous genetic (Georgiadis et al, 2014) and morphological studies (Minos et al, 2013) on three different Spicara species. It is thus hypothesized that although being supplied from almost the same locations in Turkey's coastal waters, the current discrepancies related to the reports on the interspecific relationships in Spicara genus is most likely due to the inaccurate morphological descriptions from previous studies.…”

Section: Species Divergence and Phylogenetic Relationshipssupporting

confidence: 85%

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Bektaş¹,

Aksu²,

Kalaycı³

et al. 2018

Turk. J. Fish. Aquat. Sci.

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Interspecific and intraspecific differentiation of the picarel in Turkish coastal waters were examined using partial 16S rRNA (1021 bp) and whole cytochrome b gene (1141 bp) sequences of 244 samples from 7 picarel populations across their geographical distribution. Genetic distances and phylogenetic tree topologies revealed that three Spicara species were distinctly separated from each other and S. flexuosa and S. maena are genetically more closely related than S. smaris. Lowlevel genetic diversity and a star-like haplotype network can be attributed to the founder effect associated with demographic bottleneck in late Pleistocene Mediterranean basin. AMOVA of the genetic substructure for S. flexuosa does not support any grouping in the Turkish waters. The divergence time between the Mediterranean and Black Sea populations (0.015%, cyt b) of S. flexuosa estimated based on the mtDNA clock calibration of 2% sequence per million years suggests that the Mediterranean samples with reduced genetic diversity has colonized into the Black Sea through straits during the early Holocene (about 7500 kya). The current distribution and demographic pattern of Spicara species in the Eastern Mediterranean basin are shaped by climatic events during late Pleistocene and mid-Holocene (about 25-5 kya) and the biological and ecological characteristics specific to Spicara species.

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Section: Species Divergence and Phylogenetic Relationshipssupporting

confidence: 85%

Untitled

Bektaş¹,

Aksu²,

Kalaycı³

et al. 2018

Turk. J. Fish. Aquat. Sci.

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“…Interestingly, other studies along the Turkish coast, consider S. flexuosa and S. maena to be conspecific (Karakulak et al, 2006;Soykan et al, 2010;Keskin et al, 2011;Saygılı et al, 2016;Froese and Pauly, 2017). The result of this study indicates that the distinction of the three taxa under Spicara species is possible, as shown in previous studies (Chiba et al, 2009;Imsiridou et al, 2011;Georgiadis et al, 2014;Bektaş et al, 2018).…”

Section: Genetic Differentiation Of Spicara Maena Spicara Flexuosa and Spicara Smarissupporting

confidence: 87%

“…Consequently, some studies (Quero et al, 2003;Eschmeyer, 2010;Froese and Pauly, 2020) suggest that S. maena and S. flexuosa should be considered as synonyms whereas others (Tortonose, 1986;Fischer et al, 1987;Costa, 1991;Louisy, 2002;Golani et al, 2006;Vasileva, 2007;Bilecenoğlu et al, 2014) support the distinction of the two species. More recent studies based on both genetic (Chiba et al, 2009;Imsiridou et al, 2011;Georgiadis et al, 2014;Bektaş et al, 2018) and morphological data (Minos et al, 2013) also support the latter conclusion. The discrepancy is reflected in various fish-related taxonomic databases as well.…”

Section: Introductionmentioning

confidence: 71%

Molecular characterization and phylogeography of Mediterranean picarels (Spicara flexuosa, S. maena and S. smaris) along the coasts of Turkey and the Eastern Mediterranean

Şalcıoğlu

Gubili²,

Krey³

et al. 2021

Regional Studies in Marine Science

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In this study, molecular taxonomy associated with Spicara flexuosa, Spicara maena, and Spicara smaris was examined with a geographical focus along the coasts of the Turkey and the Mediterranean. In addition, the effects of the Turkish Straits System on the evolutionary history and phylogeography of Spicara flexuosa were investigated.The mitochondrial cytochrome c oxidase I, cytochrome b, and the nuclear Interphotoreceptor retinoid-binding protein genes were used for these purposes. Our results indicated that the distinction of the three taxa under Spicara is possible with the two different mitochondrial DNA markers. Nuclear DNA analyses indicated that reproductive isolation of the S. maena and S. flexuosa was complete. Demographic analyses support the sudden population growth of S. flexuosa after a potential bottleneck. The result of the dating analyses suggested that the three Spicara species were differentiated during the early or middle Pliocene. An absence of genetic structure between Spicara flexuosa subpopulations from Turkey indicated the connectivity, within sampling locations, suggesting that the Turkish Straits System is a corridor for gene flow for this species. As picarel populations have experienced rapid decline in their distribution areas in recent years, separate population studies are necessary to help make informed conservation and management decisions for S. maena and S. flexuosa.

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“…Georgiadis et al. (2014) and Rocha‐Olivares and Chávez‐González (2008) designed assays using a multiplex‐haplotype‐specific‐PCR method that were specific enough to identify diagnostic point mutations.…”

Section: Fish Orders and Detection Methodsmentioning

confidence: 99%

“…The technique is low-cost, rapid, and practical (as it does not require complicated laboratory equipment) (Damasceno et al, 2016). Georgiadis et al (2014) and Rocha-Olivares and Chávez-González (2008) designed assays using a multiplex-haplotype-specific-PCR method that were specific enough to identify diagnostic point mutations.…”

Section: 26mentioning

confidence: 99%

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

Singh,

Young,

Hellberg

et al. 2024

Comp Rev Food Sci Food Safe

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Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA‐based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer‐probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay‐based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA‐based method was real‐time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species‐specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA‐based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.

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Melt-curve-multiplex-haplotype-specific-PCR, a valuable tool for biological studies: Application in congeneric species discrimination assay

Cited by 3 publications

References 22 publications

Untitled

Untitled

Molecular characterization and phylogeography of Mediterranean picarels (Spicara flexuosa, S. maena and S. smaris) along the coasts of Turkey and the Eastern Mediterranean

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

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