Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway.
Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
Mol Ecol Resour. 2017 Jul;17(4):742-751. doi: 10.1111/1755-0998.12623. Epub 2016 Dec 15.
The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.
从考古材料中进行全基因组规模的研究的可行性在很大程度上取决于获取内源性、真实 DNA 的能力。在大多数情况下，这最多代表 DNA 提取物的百分之几。最近已经开发了一些针对骨粉的特定预提取方案，旨在在文库扩增之前提高古 DNA 的回收。在这里，我们测试了两种此类方案（漂白洗涤和预消化步骤）组合对 12 个年龄在 750-1350 cal. 年前的大西洋鳕鱼和家养马骨样本的影响。使用高通量测序，我们表明，漂白洗涤和预消化的组合始终比单独使用这些方法中的任何一种方法产生具有更高内源性含量的 DNA 文库。此外，这些文库的分子复杂性得到了改善，内源性 DNA 模板的大小分布更大。其他文库特征，如 DNA 损伤谱或微生物群落的组成，受预提取方案的影响很小。本研究中提出的组合方案的应用将促进越来越多的古代遗骸的遗传分析，并降低全基因组测序的成本。
