Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

E E Nielsen; J A T Morgan; S L Maher; J Edson; M Gauthier; J Pepperell; Bonnie J Holmes; M B Bennett; J R Ovenden

doi:10.1111/1755-0998.12580

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Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Journal article

Peer reviewed

Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

E E Nielsen, J A T Morgan, S L Maher, J Edson, M Gauthier, J Pepperell, Bonnie J Holmes, M B Bennett and J R Ovenden

Molecular Ecology Resources, Vol.17(3), pp.431-442

2017

DOI: https://doi.org/10.1111/1755-0998.12580

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Abstract

archived tissue sample

DNA capture

DNA extraction

qPCR

shark

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

Details

Title: Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material
Authors: E E Nielsen (Author)
J A T Morgan (Author) - University of Queensland
S L Maher (Author) - University of Queensland
J Edson (Author) - University of Queensland
M Gauthier (Author) - University of Queensland
J Pepperell (Author)
Bonnie J Holmes (Author) - University of Queensland
M B Bennett (Author) - University of Queensland
J R Ovenden (Author) - University of Queensland
Publication details: Molecular Ecology Resources, Vol.17(3), pp.431-442
Publisher: Wiley-Blackwell Publishing Ltd.
Date published: 2017
DOI: 10.1111/1755-0998.12580
ISSN: 1755-098X
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering
Language: English
Record Identifier: 99450831902621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Biochemistry & Molecular Biology; Ecology; Evolutionary Biology

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