Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing
Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing
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DOI：
10.1111/1755-0998.12470
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发表时间：
2016-03-01
影响因子：
7.7
通讯作者：
Orlando, Ludovic
中科院分区：
文献类型：
--
作者：
Gamba, Cristina;Hanghoj, Kristian;Orlando, Ludovic
可以从考古和古生物遗迹中提取的DNA分子往往被降解，并被环境微生物物质大量污染。尽管高通量测序（HTS）的测序成本降低，但这降低了鸟枪法测序古代基因组的效率。因此，提高DNA提取和纯化步骤中内源性分子的回收率有助于推进古代基因组的表征。在这里，我们将三种最常用的DNA提取方法应用于五个古老的骨骼样本，这些骨骼样本跨越了近似3万年的时间范围，来自从南美洲到阿拉斯加的各种环境。我们表明，使用硅胶柱的DNA片段的纯化的基础上的方法是更有利的，比在溶液中的方法，不仅增加了回收的DNA分子的总量，但也内源性DNA片段及其分子多样性的相对重要性。因此，这些方法为下游应用提供了具有成本效益的解决方案，包括HTS平台上的DNA测序。
The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a similar to 30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.