Institute of Human Genetics, University of Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.
J Appl Genet. 2013 Aug;54(3):309-25. doi: 10.1007/s13353-013-0145-1. Epub 2013 Apr 4.
We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC-124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a "bacterial fingerprint", discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.
我们首次将下一代测序（NGS）技术应用于埃及木乃伊。从五个随机选择的第三中间到希腊罗马埃及木乃伊（公元前 806 年至公元 124 年）和两个出土的前接触玻利维亚低地骨骼中获得了七个 NGS 数据集，并对其进行了生成和特征描述。将这些数据集与三个最近发表的来自寒冷气候地区的 NGS 数据集进行了对比，即 Saqqaq、丹尼索瓦人和阿尔卑斯冰人。分析使用每个新生成或发布的数据集的一百万条读取。Blastn 和 megablast 结果使用 MEGAN 软件进行分析。在专门的古 DNA 实验室中，通过特定和敏感的聚合酶链反应（PCR）协议复制了独特的 NGS 结果。在这里，我们提供了埃及木乃伊中真实 DNA 的明确鉴定。NGS 数据集显示了组织中内源性 DNA 的不同含量。五个木乃伊中有三个显示出与 Saqqaq 永久冻土保存标本的人类读取计数相当的人类 DNA 比例。此外，还显示了木乃伊特有的宏基因组特征。通过应用“细菌指纹”，可以区分木乃伊和埃及以外温暖地区的其他遗骸。由于缺乏适当的环境监测，在分析同一木乃伊相隔 1.5 年后的不同活检时，发现了细菌大量繁殖。所有木乃伊数据集的植物王国代表都是独特的，可以部分与它们在包埋材料中的使用相关联。最后，NGS 数据显示了恶性疟原虫和刚地弓形虫 DNA 序列的存在，表明这些木乃伊中存在疟疾和弓形体病。我们证明可以从木乃伊中提取内源性古代 DNA 并将其用作 NGS 技术的合适模板，从而为未来对古埃及个体进行基因组测序开辟了新的研究途径。
