Real‐time<scp>PCR</scp>identification of lake whitefish<i>Coregonus clupeaformis</i>in the<scp>L</scp>aurentian<scp>G</scp>reat<scp>L</scp>akes

Overdyk, Lauren M.; Braid, Heather E.; Naaum, Amanda M.; Crawford, Stephen S.; Hanner, Robert

doi:10.1111/jfb.12922

Cited by 7 publications

(3 citation statements)

References 45 publications

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“…For example, the Coregonus members demonstrates recent evolutionary divergence and exhibits extensive interspecies COI haplotype sharing [7,27–29]. This genus is extremely difficult to identify morphologically as individuals from the same species exhibit multiple different morphologies within the same lake [29,30]. As well, DNA barcoding has had several limitations with identifying individuals from Coregonine to the genus and/or species level due to decreased mitochondrial DNA variation between species [7,27].…”

Section: Discussionmentioning

confidence: 99%

Development and validation of probe-based multiplex real-time PCR assays for the rapid and accurate detection of freshwater fish species

et al. 2019

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Reliable species identification methods are important for industrial environmental monitoring programs. Probe based real-time quantitative polymerase chain reaction (qPCR) provides an accurate, cost-effective and high-throughput method for species identification. Here we present the development and validation of species-specific primers and probes for the cytochrome c oxidase (COI) gene for the identification of eight ecologically and economically important freshwater fish species: lake whitefish (Coregonus clupeaformis), yellow perch (Perca flavescens), rainbow smelt (Osmerus mordax), brook trout (Salvelinus fontinalis), smallmouth bass (Micropterus dolomieu), round whitefish (Prosopium cylindraceum), spottail shiner (Notropis hudsonius) and deepwater sculpin (Myoxocephalus thompsonii). In order to identify novel primer-probe sets with maximum species-specificity, two separate primer-probe design criteria were employed. Highest ranked primer-probe sets from both methods were assayed to identify sequences that demonstrated highest specificity. Specificity was determined using control species from same genus and non-target species from different genus. Selected primer-probe sets were optimized for annealing temperature and primer-probe concentrations to identify minimum reagent parameters. The selected primer-probe sets were highly sensitive, with DNA concentrations as low as 1 ng adequate for positive species identification. A decoder algorithm was developed based on the cumulative qPCR results that allowed for full automation of species identification. Blinded experiments revealed that the combination of the species-specific primer/probes sets with the automated species decoder resulted in target species identification with 100% accuracy. We also conducted a cost/time comparison analysis between the qPCR assays established in this study with other species identification methods. The qPCR technique was the most cost-effective and least time consuming method of species identification. In summary, probe-based multiplex qPCR assays provide a rapid and accurate method for freshwater fish species identification, and the methodology established in this study can be utilized for various other species identification initiatives.

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Section: Discussionmentioning

confidence: 99%

Development and validation of probe-based multiplex real-time PCR assays for the rapid and accurate detection of freshwater fish species

et al. 2019

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“…First, C. huntsmani was recognized as a sister species to the other Coregonus species; second, Stenodus is probably a separate genus rather than a subgenus within Coregonus . Species such as Coregonus artedi , Coregonus hoyi , Coregonus kiyi , Coregonus nigripinnis, and Coregonus zenethicus , according to their data, are not related as previously thought [ 338 , 339 , 340 , 341 ], while Coregonus pollan and Coregonus fallalis , by contrast, tend to be more conspecific [ 232 ].…”

Section: Phylogenetic Characteristics Of Salmonmentioning

confidence: 99%

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

Dysin

Shcherbakov

Николаева

et al. 2022

Genes

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The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

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“…Here, we propose a new fast real-time PCR method to distinguish between the three species. Real-time PCR using TaqMan probes has been reported by different authors as a fast and sensitive method for the identification of species (Cammà, Di Domenico, & Monaco, 2012;Di Domenico, Di Giuseppe, Wicochea Rodríguez, & Cammà, 2017;Overdyk, Braid, Naaum, Crawford, & Hanner, 2016). It does not require any postamplification step and can be easily automated allowing the analysis of large numbers of samples.…”

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confidence: 99%

A new fast real‐time PCR method for the identification of three sibling Apodemus species (A. sylvaticus, A. flavicollis, and A. alpicola) in Italy

Sozio

Curini

Pascucci

et al. 2018

Ecology and Evolution

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The identification of field mice Apodemus flavicollis, Apodemus sylvaticus, and Apodemus alpicola represents a challenge for field scientists due to their highly overlapping morphological traits and habitats. Here, we propose a new fast real‐time PCR method to discriminate the three species by species‐specific TaqMan assays. Primers and probes were designed based on the alignment of 54 cyt‐b partial sequences from 25 different European countries retrieved from GenBank. TaqMan assays were then tested on 133 samples from three different areas of Italy. Real‐time PCR analysis showed 92 samples classified as A. flavicollis, 13 as A. sylvaticus, and 28 as A. alpicola. We did not observe any double amplification and DNA sequencing confirmed species assignment obtained by the TaqMan assays. The method is implementable on different matrices (ear tissues, tail, and blood). It can be used on dead specimens or on alive animals with minimally invasive sampling, and given the high sensitivity, the assay may be also suitable for degraded or low‐DNA samples. The method proved to work well to discriminate between the species analyzed. Furthermore, it gives clear results (amplified or not) and it does not require any postamplification handling of PCR product, reducing the time needed for the analyses and the risk of carryover contamination. It therefore represents a valuable tool for field ecologists, conservationists, and epidemiologists.

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Real‐timePCRidentification of lake whitefishCoregonus clupeaformisin theLaurentianGreatLakes

Cited by 7 publications

References 45 publications

Development and validation of probe-based multiplex real-time PCR assays for the rapid and accurate detection of freshwater fish species

Development and validation of probe-based multiplex real-time PCR assays for the rapid and accurate detection of freshwater fish species

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

A new fast real‐time PCR method for the identification of three sibling Apodemus species (A. sylvaticus, A. flavicollis, and A. alpicola) in Italy

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