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Identification of ancient viruses from metagenomic data of the Jomon people

Abstract

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.

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Acknowledgements

We thank the members of the Human Genetics Laboratory at the National Institute of Genetics for providing many suggestions. This project was supported by Deciphering Origin and Establishment of Yaponesians mainly based on genome sequence data project (Yaponesia Genome Project) supported by JSPS KAKENHI Grant Number JP 18H05506. Some computations were performed on the NIG supercomputer at ROIS National Institute of Genetics. We would like to thank Enago (https://www.enago.jp) for English editing. This work was supported in part by The Graduate University for Advanced Studies, SOKENDAI.

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Correspondence to Ituro Inoue.

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Nishimura, L., Sugimoto, R., Inoue, J. et al. Identification of ancient viruses from metagenomic data of the Jomon people. J Hum Genet 66, 287–296 (2021). https://doi.org/10.1038/s10038-020-00841-6

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