Phylogenomic analyses from archival DNA

世界各地的博物馆收藏了数百万件标本，作为各种研究领域的参考。样品的处理通常涉及甲醛(FA)作为固定剂。虽然样品的固定和随后的保存允许许多形态特征的保存，但样品的DNA会受到破坏，因为FA在DNA分子以及DNA和蛋白质之间引入了交联链，抑制了使用DNA扩增的技术，包括所有现有的DNA测序技术。此外，固定FA和随后的乙醇储存会通过脱氨作用严重降解DNA，导致严重的碎裂。因此，档案DNA(ArcDNA)样本与古代DNA(ADNA)具有许多共同的特征。在这个项目中，我们打算将所有当前关于固定样本的FA特定处理的知识与DNA提取协议结合起来，专注于捕获非常短的DNA片段(&lt；100个碱基对)。这些短片段必须被合并到DNA文库中。最有希望的方法是用单链DNA构建文库，这种方法可以直接测序，或者适合于更具体的步骤，如杂交浓缩。我们的最终目标是建立一种成本和时间高效的、普遍适用的DNA提取方法，用于从档案DNA文库，特别是从FA固定样本中成功地提取和靶向捕获mt和具有系统发育信息的nDNA。在测试成功后，我们将重点放在博物馆的深海灯鲨(Etmopteridae)样本上。这些鲨鱼完美地例证了对稀有物种进行分子分析时出现的典型问题，这些稀有物种在自然界中很难获得。在这里，来自博物馆样本的DNA序列信息将对分类学和系统发育分析具有重要价值。

Museum collections worldwide house millions of specimens serving as references in various fields of research. The curatorial treatment of samples often involves formaldehyde (FA) as fixative. While the fixation and subsequent preservation of samples allows for the conservation of many morphological characters, the DNA of samples is damaged as FA introduces cross-links between DNA molecules as well as DNA and proteins, inhibiting techniques that employ amplification of DNA, including all currently available DNA sequencing techniques. Further, FA fixation and subsequent ethanol storage heavily degrade DNA by depurination, causing severe fragmentation. Therefore, archival DNA (arcDNA) samples share many characters with ancient DNA (aDNA). In this project, we intend to combine all current knowledge on FA specific treatments of fixed samples with aDNA extraction protocols focusing on capturing very short DNA fragments (<100 basepairs). These short fragments have to be incorporated into a DNA library. The most promising way are library constructions from single stranded DNA, which can be directly sequenced or, alternatively, are suitable for more specific steps, such as hybrid enrichment. Our ultimate goal is the establishment of a cost- and time efficient, universally applicable protocol for successful DNA extraction and target capture of mt and phylogenetically informative nDNA from archival DNA libraries, especially from FA fixed samples. After successful testing, we focus on museum samples of deep-sea lantern sharks (Etmopteridae). These sharks perfectly exemplify typical issues arising with molecular analyses of rare species, which are difficult to access in nature. Here, DNA sequence information from museum samples would be of great value for taxonomic and phylogenetic analyses.