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 assess and optimize 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/基因组分析的珍贵DNA来源。然而，目前针对提取方法的评估与优化工作仍较为匮乏，而该环节对下游应用至关重要。本研究针对鲨鱼体内储量丰富的馆藏骨骼材料展开评估与优化，以确定其作为时序基因组研究的DNA来源的实用性。本研究采用6种不同的DNA提取方法（涵盖2种商业试剂盒与3种实验方案），对现代及馆藏虎鲨（Galeocerdo cuvier）的颌骨与椎骨样本，即所谓的"生物碎屑（bio-swarf）"进行处理。本研究采用实时定量PCR（qPCR）方法，对不同方案的DNA得率与质量进行比较。针对颌骨碎屑，所有方法均能获得较高的DNA得率与质量；而对于椎骨样本，不同方案间的得率差异显著。大白鲨（Carcharodon carcharias）样本也得到了相似的实验结果。将优化后的方法应用于38份可追溯至1912年的馆藏及私人垂钓战利品标本时，68%的样本可获得满足下游基因组分析需求的DNA。未观察到样本保存年限与DNA质量、得率之间存在明确关联，这大概率反映了这些战利品标本在制备与储存环节的差异。采用20000个捕获探针对DNA捕获基因组文库进行的初步测序结果显示，大部分捕获序列均来源于虎鲨。本研究证实，馆藏鲨鱼颌骨与椎骨是可用于大规模基因组分析的高得率DNA潜在来源。本研究同时表明，即便针对同类组织类型，对提取方案进行严谨评估也可大幅提升DNA得率。