Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
Sci Rep. 2011;1:74. doi: 10.1038/srep00074. Epub 2011 Aug 24.
The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.
第二代测序技术的发展极大地促进了古 DNA（aDNA）领域的发展。通过使用靶向捕获富集方法，可以进一步利用其应用，克服古样本中内源性和污染 DNA 含量低带来的限制。我们在古玉米构建的 Illumina 测序文库上测试了 Agilent 的 SureSelect 和 Mycroarray 的 MySelect 溶液捕获系统的性能，以确定影响 aDNA 捕获实验的关键因素。无论捕获方法如何，捕获靶标中的高克隆性和多拷贝序列的存在都会导致数据偏倚。就平均目标富集而言，两种方法都没有表现出一致性的优势，当比较两种平铺设计时，也没有观察到明显的差异。除了证明从古代植物材料中捕获 aDNA 的合理性之外，我们的结果还为那些计划对 aDNA 进行靶向测序的人提供了有用的建议。
