An accurate and rapid method for species identification in plants: Melting fingerprint-high resolution melting (MFin-HRM) analysis

Buddhachat, Kittisak; Changtor, Phanupong; Ninket, Sunatcha

doi:10.1016/j.plgene.2019.100203

Cited by 9 publications

(3 citation statements)

References 33 publications

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“…Analizy HRM ze względu na niski koszt i zastosowanie dostępnego oprzyrządowania prawdopodobnie wypełnią niszę w regionach i laboratoriach o mniejszych zasobach, ale także będą uzupełnieniem technologii sekwencjonowania. Genotypowanie gatunków roślin [24][25][26][27][28][29] Identyfikacja gatunkowa mikroorganizmów [30,31] Genotypowanie w obrębie gatunków drobnoustrojów [32] Bar-HRM Uwierzytelnianie żywności i produktów ziołowych [19,20] Kontrola jakości warzyw, rozróżnienie roślin jadalnych i trujących [21,33] MS-HRM Wykrywanie biomarkerów nowotworowych [34,35] Diagnozowanie chorób imprintowanych [35] Kliniczna weryfikacja wyników badań epigenomu [36] Ocena metylacji w zastosowaniach diagnostycznych i badawczych [22,37] MFin-HRM Identyfikacja i uwierzytelnianie gatunków [23,38] High Resolution Melting Analysis (HRM-PCR) -method and its application…”

Section: Podsumowanieunclassified

Technologia HRM-PCR; denaturacja DNA z wysoką rozdzielczością opis oraz zastosowanie

2021

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Denaturacja DNA z wysoką rozdzielczością – HRM (z ang. High Resolution Melt) jest metodą opartą na identyfikacji różnic w denaturacji produktów reakcji PCR w obecności barwników fluorescencyjnych. Stosowana jest do wykrywania zmienności genetycznej w sekwencjach kwasów nukleinowych, w wielu gałęziach nauki, medycyny i przemysłu. Artykuł ten stanowi przegląd literatury dotyczącej metodyki, zastosowań oraz rozwoju analizy HRM, która dzięki zaletom takim jak szybkość, niski koszt, elastyczność i prostota znalazła wiele zastosowań, których spektrum wciąż się powiększa.

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Section: Podsumowanieunclassified

Technologia HRM-PCR; denaturacja DNA z wysoką rozdzielczością opis oraz zastosowanie

2021

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“…Perhaps, in several areas, the specimens obtained have been incomplete forms, immature stage, or modi ed/processed samples without key characters to identify, contributing to di culty/impossibility in species identi cation and hampering the advance of investigation or research 9 . In several decades ago, advanced molecular approaches e.g., hybridization, DNA ngerprint, DNA barcodes, high resolution melting (HRM) have been used widely and extensively for facilitating species authentication in various organisms [2][3][4][5][6][10][11][12][13][14][15][16] . Certainly, these molecular approaches enable species identi cation despite the specimens with completely damaged but DNA existing, especially DNA barcodes (Bar) which there are many regions exhibiting a successful species discrimination for plant species (e.g., rbcL, matK, trnL, and ITS) [15][16] .…”

Section: Introductionmentioning

confidence: 99%

Bar-cas12a, a Novel and Rapid Method for Plant Species Authentication: A Case of Phyllanthus Species

Buddhachat

Paenkaew

Sripairoj

et al. 2021

Preprint

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The rapid and accurate species diagnosis accelerates the performance to investigate various biology fields and its relevant, perhaps but morphology-based species taxonomy/identification hamper. DNA barcodes (Bar) has been employed extensively for plant species identification. Recently, CRISPR-cas system can be applied for diagnostic tool to detect pathogen’s DNA based on the collateral activity of cas12a or cas13. Here, we developed barcode-hyphenated with cas12a assay, “Bar-cas12a” for species authentication using Phyllanthus amarus as a model. The gRNAs were designed from trnL region, namely gRNA-A and gRNA-B. As a result, gRNA-A was highly specific to P. amarus amplified by RPA in contrast to gRNA-B even in contaminated condition. Apart from the large variation of gRNA-A binding in DNA target, cas12a- specific PAM’s gRNA-A as TTTN can be found only in P. amarus. PAM site may be recognized one of the potential regions for increasing specificity to authenticate species. In addition, the sensitivity of Bar-cas12a using both gRNAs gave the same detection limit at 0.8 fg and it was 1,000 times more sensitive compared to agarose gel electrophoresis. Overall, Bar-cas12a using trnL-designed gRNA offer a highly specific, sensitive, speed, and simple approach for plant species authentication and is likely to implement point-of-care testing.

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“…Several studies have reported on the successful identification of plant and bacteria species using HRM with DNA fingerprinting including Phyllanthus amarus ( Tulsiani et al., 2010 ) and Leptospira spp. ( Buddhachat, Changtor & Ninket, 2019 ; Naze et al., 2015 ). Melting profiles can be measured in real time using the universal ISSR primer combined with specific software that can be employed to explore and quantify them in order to reduce the subjective errors that are associated with human biases ( Power, 1996 ; Tulsiani et al., 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic variations and dog breed identification using inter-simple sequence repeat markers coupled with high resolution melting analysis

Kriangwanich

Nganvongpanit

Buddhachat

et al. 2020

PeerJ

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The identification of differing physical characteristics of dogs is an uncomplicated and straightforward way to categorize dog breeds. However, many dog owners and veterinarians still struggle to distinguish between pure breed and mixed variations in certain breeds of dogs. Presently, the absence of the tools and methods needed to confirm a pure breed dog is a significant problem since the only method available to validate pure or mongrel breeds is the official pedigree system. Inter-simple sequence repeat markers have been successfully used to assess genetic variations and differentiations. Notably, inter-simple sequence repeat markers coupled with high resolution melting analysis were effectively used for the breed identification of 43 breeds of dogs (total 463 dogs). The 10 primers chosen for analysis resulted in a range of 31–78.6% of breed discrimination when using one primer, while a combination of two primers was able to successfully discriminate between all of the 43 dog breeds (100%). Shannon’s index information (I = 2.586 ± 0.034) and expected heterozygosity (He = 0.908 ± 0.003) indicated a high level of genetic diversity among breeds. The fixation index (Fst) revealed a value of 10.4%, demonstrating that there was a high level of genetic subdivision between populations. This study showed that inter-simple sequence repeat marker analysis was effective in demonstrating high genetic diversity among varying breeds of dogs, while a combination of Inter-simple sequence repeat marker analysis and high resolution melting analysis could provide an optional technique for researchers to effectively identify breeds through genetic variations.

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An accurate and rapid method for species identification in plants: Melting fingerprint-high resolution melting (MFin-HRM) analysis

Cited by 9 publications

References 33 publications

Technologia HRM-PCR; denaturacja DNA z wysoką rozdzielczością opis oraz zastosowanie

Technologia HRM-PCR; denaturacja DNA z wysoką rozdzielczością opis oraz zastosowanie

Bar-cas12a, a Novel and Rapid Method for Plant Species Authentication: A Case of Phyllanthus Species

Genetic variations and dog breed identification using inter-simple sequence repeat markers coupled with high resolution melting analysis

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