More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens
More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens
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DOI：
10.1111/1755-0998.13077
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发表时间：
2020-09-01
影响因子：
7.7
通讯作者：
McCormack, John E.
中科院分区：
文献类型：
--
作者：
Tsai, Whitney L. E.;Schedl, Margaret E.;McCormack, John E.
下一代测序技术通过揭示标本作为基因组资源，极大地扩展了博物馆藏品的实用性和价值。随着博物馆基因组学领域的发展，对最大化DNA产量的提取方法的需求也在增长。对于鸟类博物馆标本，从趾垫中提取DNA的既定方法适用于大多数标本。然而，对于一些标本，特别是那些非常小或非常大的鸟类，脚趾垫可能是一个贫穷的DNA来源。在这项研究中，我们应用两种DNA提取方法（酚-氯仿和硅胶柱）的三个不同来源的DNA（趾垫，皮肤穿孔和骨）从10个历史鸟类博物馆标本。我们表明，一个修改的苯酚-氯仿方案产生了显着更多的DNA比硅胶柱方案（例如，Qiagen DNeasy Blood & Tissue Kit），适用于所有组织类型。然而，使用硅胶柱方案的提取物平均比使用苯酚-氯仿方案的提取物含有更长的片段，这可能是由于硅胶柱中小片段的损失。虽然脚趾垫产生更多的DNA比皮肤打孔和骨碎片，皮肤打孔被证明是一个可靠的替代来源的DNA，并可能特别有吸引力时，脚趾垫提取是不切实际的。总的来说，我们发现，历史鸟类博物馆标本含有大量的DNA基因组研究在大多数提取方案下，但酚-氯仿协议始终提供了大量的DNA所需的最新的基因组协议。
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.