DNA Barcodes from Snake Venom: a Broadly Applicable Method for Extraction of DNA from Snake Venoms

Smith, Cara F.; McGlaughlin, Mitchell E.; Mackessy, Stephen P.

doi:10.2144/btn-2018-0096

Cited by 8 publications

(5 citation statements)

References 49 publications

(66 reference statements)

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“…Since the inception of the Cold Code (Che et al, 2012; Murphy et al, 2013), the effectiveness of making preliminary identifications of herpetofaunal species using DNA barcodes has been increasingly shown, and it has also accelerated the development of DNA barcoding of herpetofauna (Arida et al, 2021; Bernstein et al, 2021; Chambers & Hebert, 2016; Hawlitschek et al, 2016; Laopichienpong et al, 2016; Lyra et al, 2017; Mulcahy et al, 2018; Smith et al, 2018; Trivedi et al, 2016; Vacher et al, 2020; Zangl et al, 2020). Here, we provide a DNA barcode reference library for over 80% of recognized species of Chinese snakes and identify 36 candidate species that could not be assigned to any nominal species based on morphological characters (Table S1).…”

Section: Discussionmentioning

confidence: 99%

“…For 42 species and one candidate species with multiple OTUs, maximum within-OTU genetic distances were much lower than the maximum intraspecific p-distance of the corresponding species and candidate species. Chambers & Hebert, 2016;Hawlitschek et al, 2016;Laopichienpong et al, 2016;Lyra et al, 2017;Mulcahy et al, 2018;Smith et al, 2018;Trivedi et al, 2016;Vacher et al, 2020;Zangl et al, 2020). Here, we provide a DNA barcode reference library for over 80% of recognized species of Chinese snakes and identify 36 candidate species that could not be assigned to any nominal species based on morphological characters (Table S1).…”

Section: Otu Delimitationmentioning

confidence: 99%

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DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

Hou

Yuan

et al. 2023

Molecular Ecology Resources

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DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species‐delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty‐eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

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Section: Discussionmentioning

confidence: 99%

Section: Otu Delimitationmentioning

confidence: 99%

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

Hou

Yuan

et al. 2023

Molecular Ecology Resources

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“…The presence of nucleosides in snake venom and its role in toxicity was documented but there was limited information on free nucleotides (4,5). However, it is known that snake venom contains ribonucleic acid (RNA) (63,64) and deoxyriboucleic acid (DNA) (65,66), which comes from the cells covering the lumen of the venom gland. In line with this information, it is highly possible that peaks originating from PO 2 -stretching vibrations in the FTIR spectrum arise mainly from nucleic acid backbone and nucleosides.…”

Section: Discussionmentioning

confidence: 99%

A Fourier Transform Infrared Spectroscopic Investigation of Macrovipera lebetina lebetina and M. l. obtusa Crude Venoms

İğci¹,

Demiralp²

2020

Eur J Biol

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Objective: Snake venoms are rich sources of bioactive molecules and have been investigated using various bioanalytical methods. Fourier transform infrared (FTIR) spectroscopy is a sensitive method that can be used to analyze biological samples. The aim of this study is to apply the FTIR spectroscopy method for the characterization of snake venom. Materials and Methods:The study characterized the lyophilized crude venoms of Macrovipera lebetina lebetina and M. l. obtusa by FTIR spectroscopy coupled with attenuated total reflectance (ATR) method in the mid-infrared region and compared the spectra between the two subspecies. The band area and intensity values were calculated for comparison and wavenumbers were detected by automated peak picking. Additionally, the study analyzed the secondary structure of venom proteins by using the second derivative spectra. Results:The study detected fourteen major and minor peaks in absorbance spectra which were assigned to various biomolecules such as proteins, carbohydrates, and nucleic acids. Four major sub-bands were observed in the second derivative spectra of Amide I-II region indicating different protein secondary structures. It was observed that there are some quantitative differences and peak shifts between the spectra of venoms of two subspecies, indicating the alteration of biomolecules. Conclusion:To the best of our knowledge, this is the first report of the use of the FTIR-ATR spectroscopy method focusing solely on the characterization of crude snake venoms in literature, accompanied with detailed peak assignment and protein secondary structure analysis. As a preliminary reference study, the results showed the usefulness of FTIR-ATR spectroscopy for the physicochemical characterization of lyophilized snake venom.

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“…Besides rapid species identification, this approach is also performed to detect the Molecular Taxonomic Units (MOTUs) (Tyagi et al 2017(Tyagi et al , 2019. Further, this molecular tool is also successfully evident in forensic science by naming the unknown snakes from their venoms (Sharma et al 2016;Smith et al 2018). The earlier study suggested significant genetic divergence was observed in the different population of two deadly snakes in India and other adjacent countries (Ophiophagus hannah and Bungarus fasciatus) (Kundu et al 2020).…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding elucidates the population genetic diversity of venomous cobra species (Reptilia: Elapidae) in Indo-Bangladesh region

Kundu

Lalremsanga

Rahman

et al. 2020

Mitochondrial DNA Part B

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The DNA barcode data of venomous cobra species (Naja naja and Naja kaouthia) are limited in the global database, especially from India and Bangladesh. Owing to the rapid success of DNA barcoding for discriminating a variety of species around the world, the present study aimed to generate the mitochondrial cytochrome c oxidase subunit I (COI) gene information of two morphologically identified deadly elapid species from the Mizoram state in northeast India and Rangpur in northern Bangladesh. The multiple species delimitation methods: Automatic Barcode Gap Discovery (ABGD), General Mixed Yule-Coalescent (GMYC), and Poisson-Tree-Processes (bPTP) revealed 14, 16, and 18 molecular operational taxonomic units (MOTUs) for 12 Naja species. The binocellate cobra, N. naja showed monophyletic clustering in both maximum-likelihood (ML) and Bayesian (BA) trees, single MOTU in ABGD and GMYC, and negligible intra-species genetic distance (0.2%) with two haplotypes. However, the monocellate cobra, N. kaouthia showed paraphyletic and polytomy in ML and BA phylogenies respectively; more than one MOTUs in ABGD, GMYC, and bPTP analyses; and sufficient intra-species genetic distances (0.6-2.3%) with five haplotypes related to the diverse geographical locations in Bangladesh, China, India, and Thailand. By superimposing the executed species delimitation criteria, the present molecularbased investigation concludes the presence of cryptic diversity of N. kaouthia in Indo-Bangladesh, China, and Thailand.

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DNA Barcodes from Snake Venom: a Broadly Applicable Method for Extraction of DNA from Snake Venoms

Cited by 8 publications

References 49 publications

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

A Fourier Transform Infrared Spectroscopic Investigation of Macrovipera lebetina lebetina and M. l. obtusa Crude Venoms

DNA barcoding elucidates the population genetic diversity of venomous cobra species (Reptilia: Elapidae) in Indo-Bangladesh region

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