Discriminating European cyprinid specimens by barcode high-resolution melting analysis (Bar-HRM)—A cost efficient and faster way for specimen assignment?

Behrens-Chapuis, Simone; Malewski, Tadeusz; Suchecka, Ewa; Geiger, Matthias F.; Herder, Fabian; Bogdanowicz, Wiesław

doi:10.1016/j.fishres.2018.02.007

Cited by 21 publications

(15 citation statements)

References 92 publications

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“…Here, we have validated the use of HRM for the analysis of field eDNA samples (as opposed to use for optimisation only 40,91 ), which is still incipient, both for water and sediment, although this method has been extensively used as a highly discriminative method for identifying species 39,92,93 . We have observed that the use of the same primers can present problems when the amount of eDNA from one of the species is considerably larger than for the other.…”

Section: Discussionmentioning

confidence: 99%

Effect of artificial barriers on the distribution of the invasive signal crayfish and Chinese mitten crab

Robinson

Leániz

Consuegra

2019

Sci Rep

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The role of river obstacles in preventing or facilitating the dispersal and establishment of aquatic invasive species is controversial. Novel detection tools like environmental DNA (eDNA) can be used for monitoring aquatic invasive species (AIS) such as the American signal crayfish ( Pacifastacus leniusculus ) and the Chinese mitten crab ( Eriocheir sinensis ), providing information on the effect of barriers on their distribution. We analysed eDNA from both water and surface sediment in three river catchments (Medway, Dee and Stour; Great Britain), with differing levels of connectivity, to determine spatial distribution of the two species, and assessed the effect of barriers on their eDNA detection. Positive eDNA detections were obtained within confirmed sites for both species in all catchments, with evidence of species overlap in the River Medway. Upstream barriers in the Medway positively influenced detection success of mitten crab lower in the catchment while detection success of signal crayfish was higher in the highly fragmented catchment (River Medway). This information on the role of river barriers on AIS distribution and eDNA detection is important for management strategies and for predicting both future dispersal and likelihood of new colonisations in previously uninvaded fragmented catchments.

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Section: Discussionmentioning

confidence: 99%

Effect of artificial barriers on the distribution of the invasive signal crayfish and Chinese mitten crab

Robinson

Leániz

Consuegra

2019

Sci Rep

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“…The significant outcome of these tests indicates that shape, amplitude and melting peak do not just vary by chance [ 24 ]. The sensitivity of this method is known to account for single nucleotide differences [ 8 ]. The observed consistent differences in melting and fluorescence curves allow for the discrimination of species based on their melting profiles by eye.…”

Section: Resultsmentioning

confidence: 99%

“…Quantitative real time PCR and subsequent HRM analyses were conducted in a Rotor-Gene 3000 thermal cycler (Corbett Research, Mortlake, New South Wales, Australia). PCR reactions using the Real Time 2 × PCR Master Mix EvaGreen (A & A Biotechnology, Gdynia, Poland) and cycling conditions followed [ 8 ], only altering the annealing temperature to 49 °C. Optical measurements at 510 nm were recorded during each extension step.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, mini-barcodes can be combined with high resolution melting analysis (bar-HRM), which provides a time- and cost-effective way to discriminate DNA sequences with small, even single, nucleotide differences, thus avoiding the need of sequencing, which is the costliest step in standard DNA barcoding. The method is particularly suited for fast discrimination of a limited number of species [ 8 ]. Briefly, following a real-time PCR, the products are denatured by increased temperature and the changes in fluorescence caused by the release of an intercalating dye from the DNA duplex are measured [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

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Discriminating larvae of two syntopic Cychramus species (Coleoptera, Nitidulidae) by means of bar-HRM analysis

Zangl

Oberreiter

Huss³

et al. 2020

Mol Biol Rep

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Molecular genetic methods are increasingly used to supplement or substitute classical morphology-based species identification. Here, we employ a COI mini-barcode coupled high-resolution melting analysis to quickly, cost-efficiently and reliably determine larvae of two closely related Cychramus (Coleoptera, Nitidulidae) species. Euclidean distance comparison (p < 0.01) and a Welch t-test of the melting point temperatures (p < 0.01) provide highly significant statistical evidence for species specific differences in melting and fluorescence curves, thus allowing the assignment of larvae to either of the two species. This protocol serves as a fast, low-cost and low-tech method to discriminate between pairs or groups of closely related species and can be adapted and applied to various ecological research questions.

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“…The use of molecular methods, such as the bar code of mitochondrial DNA (mtDNA) and the genotyping of nuclear DNA, has made it possible to reduce errors in the identification of species, as well as to resolve phylogenetic relationships by revealing distribution patterns of wild canids. (Ochoa, ; Tchaicka et al, ; Torés, ) to the more recent use of barcode regions of cytochrome B (Behrens‐Chapuis et al, ; Fernandes, Costa, Oliveira, & Mafra, ; Jeon, Anderson, Won, Lim, & Suk, ; Wang et al, ; Yacoub, Fathi, & Mahmoud, ).…”

Section: Introductionmentioning

confidence: 99%

High‐resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile

Anabalón

Encina‐Montoya

Sánchez

et al. 2019

Ecology and Evolution

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Easy, economic, precise species authentication is currently necessary in many areas of research and diagnosis in molecular biology applied to conservation studies of endangered species. Here, we present a new method for the identification of three fox species of the Lycalopex genus in Chile. We developed an assay based on high‐resolution melt analysis of the mitochondrial cytochrome B gene, allowing a simple, low cost, fast, and accurate species determination. To validate the assay applicability for noninvasive samples, we collected fecal samples in the Atacama Desert, finding unexpectedly one species outside of its known distribution range. We conclude that the assay has a potential to become a valuable tool for a standardized genetic monitoring of the Lycalopex species in Chile.

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Discriminating European cyprinid specimens by barcode high-resolution melting analysis (Bar-HRM)—A cost efficient and faster way for specimen assignment?

Cited by 21 publications

References 92 publications

Effect of artificial barriers on the distribution of the invasive signal crayfish and Chinese mitten crab

Effect of artificial barriers on the distribution of the invasive signal crayfish and Chinese mitten crab

Discriminating larvae of two syntopic Cychramus species (Coleoptera, Nitidulidae) by means of bar-HRM analysis

High‐resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile

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