Nishimura Luca, Sugimoto Ryota, Inoue Jun, Nakaoka Hirofumi, Kanzawa-Kiriyama Hideaki, Shinoda Ken-Ichi, Inoue Ituro
Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan.
Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan.
J Hum Genet. 2021 Mar;66(3):287-296. doi: 10.1038/s10038-020-00841-6. Epub 2020 Sep 30.
Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.
古DNA研究提供了有关古代人类起源、种群结构和身体特征的基因组信息，而这些信息无法仅通过考古研究来考察。从古代人类骨骼、牙齿或组织中提取的DNA常常被共存的细菌和病毒基因组污染，这些基因组包含来自感染古代人类的古代微生物的DNA。古代病毒基因组的信息有助于推断病毒的进化。在此，我们利用了来自5名绳文人牙髓的宏基因组测序数据，这些人生活在3000多年前的日本列岛，目的是检测古代病毒基因组。我们对非人类读数进行了从头组装，获得了277387条长度超过1000bp的重叠群。这些重叠群与一组现代病毒基因组序列进行了同源性搜索。我们能够检测到11个推定的古代病毒基因组。其中，我们重建了Siphovirus contig89（CT89）病毒基因组的完整序列。绳文CT89样序列被确定包含59个开放阅读框，其中已知编码噬菌体蛋白的5个基因处于强烈的纯化选择之下。CT89的宿主预计是Schaalia meyeri，一种存在于人类口腔中的细菌。最后，CT89系统发育树显示出两个簇，绳文序列与这两个簇均分离。我们的结果表明，绳文人牙髓的宏基因组信息对于检索用于研究其进化的古代病毒基因组至关重要。
