Mak Sarah Siu Tze, Gopalakrishnan Shyam, Carøe Christian, Geng Chunyu, Liu Shanlin, Sinding Mikkel-Holger S, Kuderna Lukas F K, Zhang Wenwei, Fu Shujin, Vieira Filipe G, Germonpré Mietje, Bocherens Hervé, Fedorov Sergey, Petersen Bent, Sicheritz-Pontén Thomas, Marques-Bonet Tomas, Zhang Guojie, Jiang Hui, Gilbert M Thomas P
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.
Gigascience. 2017 Aug 1;6(8):1-13. doi: 10.1093/gigascience/gix049.
Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
随着下一代测序平台的发展，古DNA研究发生了革命性变化。尽管已有多种此类平台应用于古DNA样本，但Illumina系列如今仍是主要选择，主要原因是其产量高且读长较短。最近，一种用于古基因组数据生成的潜在有吸引力的替代平台——BGISEQ - 500已被开发出来，其序列输出与Illumina系列相当。在本研究中，我们专门针对降解DNA对标准BGISEQ - 500文库制备方法进行了改进，然后将BGISEQ - 500与Illumina HiSeq2500平台在从8个历史时期和古代的狗及狼样本中提取的DNA上的测序性能和数据质量进行了直接比较。两个测序平台生成的数据在很大程度上具有可比性，在内源核DNA水平（P = 0.371）、平均序列长度（P = 0.718）、序列GC含量（P = 0.311）、双链DNA损伤率（P = 0.309）和序列克隆性（P = 0.093）等参数方面未观察到统计学上的显著差异。在单链DNA损伤率（δS；BGISEQ - 500略低，P = 0.011）和与参考基因组的背景差异率（θ；BGISEQ - 500略高，P = 0.012）方面发现了小的显著差异。这可能是由于用于聚合酶链反应扩增文库的扩增循环次数不同所致。在线粒体DNA回收率方面也观察到了显著差异（P = 0.018），不过我们认为这可能是一种随机效应，与从3个内源性DNA总体水平极低的样本中测序的线粒体水平极低有关。尽管我们承认我们的分析仅限于动物材料，但我们的观察结果表明，BGISEQ - 500有潜力成为一个有效且可能有价值的古基因组数据生成替代平台，值得对降解DNA测序和分析感兴趣的人在未来进行探索。
