title: Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.
abstract: 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.
authors: National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark.|School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: E E
authors: EE
authors: Nielsen
authors: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: J A T
authors: JAT
authors: Morgan
authors: School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: S L
authors: SL
authors: Maher
authors: Queensland Brain Institute, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: J
authors: J
authors: Edson
authors: QFAB Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: M
authors: M
authors: Gauthier
authors: Pepperell Research and Consulting Pty Ltd, Noosaville, Qld., 4566, Australia.
authors: J
authors: J
authors: Pepperell
authors: School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: B J
authors: BJ
authors: Holmes
authors: School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: M B
authors: MB
authors: Bennett
authors: School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia.
authors: J R
authors: JR
authors: Ovenden
mesh_terms: D000818:Animals; D004247:DNA / Q000302:isolation & purification*; D015723:Gene Library; D016678:Genome; D007568:Jaw; D012754:Sharks / Q000235:genetics*; D013131:Spine
chemical_list: D004247:DNA
keywords: DNA capture; DNA extraction; archived tissue samples; genomics; qPCR; shark