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

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.馆藏标本是回顾性遗传与基因组分析中极具价值的DNA来源。然而，针对DNA提取方法的评估与优化工作往往开展有限，而此类方法对下游应用可能至关重要。本研究针对鲨鱼丰富的馆藏骨骼材料作为时序基因组研究DNA来源的实用性进行了评估与优化。本研究采用6种不同的DNA提取方法（涵盖2种商用试剂盒与3种实验方案），对现代及馆藏虎鲨（Galeocerdo cuvier）颌骨与椎骨的所谓生物切屑（bio-swarf）样本进行处理，并通过定量聚合酶链式反应（quantitative PCR，qPCR）方法对比不同方案的DNA得率与质量。对于颌骨切屑样本，所有方法均能获得相对较高的DNA得率与质量；而对于椎骨样本，不同实验方案间的得率差异显著。对大白鲨（Carcharodon carcharias）的样本开展实验也得到了相似结果。将优化后的方法应用于38件可追溯至1912年的馆藏及私人垂钓战利品标本，其中68%的样本可提取到满足下游基因组分析需求的DNA。未发现样本保存年限与DNA质量、得率之间存在明确关联，这大概率与各战利品标本不同的制备及保存方式有关。使用20000条捕获探针开展DNA捕获基因组文库的测序预实验，结果显示捕获得到的序列中有相当比例源自虎鲨。本研究证实，馆藏鲨鱼颌骨与椎骨是可用于基因组规模分析的高得率潜在DNA来源。本研究同时表明，即便针对相似的组织类型，对提取方案进行细致评估也可大幅提升DNA得率。