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.

馆藏标本是开展回顾性遗传与基因组分析的珍贵DNA来源。然而，当前针对馆藏标本DNA提取方法的评估与优化工作往往较为匮乏，而此类方法对下游应用可能至关重要。本研究聚焦鲨鱼大量馆藏骨骼材料，旨在优化其作为时序基因组研究DNA来源的实用性。我们选取6种不同的DNA提取方法，涵盖2种商用试剂盒与3种提取方案，对现代及馆藏虎鲨（Galeocerdo cuvier）颌骨与脊椎骨的所谓生物碎屑（bio-swarf）样本进行处理。通过定量PCR（qPCR）方法比较不同方案的DNA得率与质量。结果显示，针对颌骨碎屑样本，所有方法均可获得较高的DNA得率与质量；而针对脊椎骨样本，不同提取方案间的得率差异显著。大白鲨（Carcharodon carcharias）样本亦得到了相似的实验结果。将优化后的提取方法应用于38份可追溯至1912年的馆藏标本及私人垂钓战利品标本，其中68%的样本可获得满足下游基因组分析需求的足量DNA。研究未观察到样本保存年限与DNA质量、得率间存在明确关联，这大概率与这些战利品不同的制备及存储方式有关。使用20000条捕获探针开展DNA捕获基因组文库的预试验测序，结果显示捕获得到的序列中有相当一部分源自虎鲨。本研究证实，馆藏鲨鱼颌骨与脊椎骨是可用于基因组规模分析的高得率DNA潜在来源；同时也表明，即便针对同类组织类型，仔细评估并优化提取方案可大幅提升DNA得率。