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DOI	10.1073/pnas.2010758118
	Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome
	Kojima S.; Yoshikawa K.; Ito J.; Nakagawa S.; Parrish N.F.; Horie M.; Kawano S.; Tomonaga K.
发表日期	2021
ISSN	00278424
卷号	118 期号:5
英文摘要	Understanding the genetics and taxonomy of ancient viruses will give us great insights into not only the origin and evolution of viruses but also how viral infections played roles in our evolution. Endogenous viruses are remnants of ancient viral infections and are thought to retain the genetic characteristics of viruses from ancient times. In this study, we used machine learning of endogenous RNA virus sequence signatures to identify viruses in the human genome that have not been detected or are already extinct. Here, we show that the k-mer occurrence of ancient RNA viral sequences remains similar to that of extant RNA viral sequences and can be differentiated from that of other human genome sequences. Furthermore, using this characteristic, we screened RNA viral insertions in the human reference genome and found virus-like insertions with phylogenetic and evolutionary features indicative of an exogenous origin but lacking homology to previously identified sequences. Our analysis indicates that animal genomes still contain unknown virus-derived sequences and provides a glimpse into the diversity of the ancient virosphere. © 2020 Proceedings of the National Academy of Sciences of the United States of America. All rights reserved.
英文关键词	Endogenous RNA virus; Human genome , paleovirology; Machine learning
语种	英语
scopus关键词	article; human; human experiment; human genome; machine learning; nonhuman; RNA virus
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/180789
作者单位	Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan; Department of Computer and Network Engineering, Graduate School of Informatics and Engineering, University of Electro-Communications, Tokyo, 182-8585, Japan; Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan; Department of Molecular Life Science, Tokai University School of Medicine, Isehara, 259-1193, Japan; Genome Immunobiology, RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, Yokohama, 230-0045, Japan; Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8507, Japan; Laboratory of RNA Viruses, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8507, Japan; Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
推荐引用方式 GB/T 7714	Kojima S.,Yoshikawa K.,Ito J.,et al. Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome[J],2021,118(5).
APA	Kojima S..,Yoshikawa K..,Ito J..,Nakagawa S..,Parrish N.F..,...&Tomonaga K..(2021).Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome.Proceedings of the National Academy of Sciences of the United States of America,118(5).
MLA	Kojima S.,et al."Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome".Proceedings of the National Academy of Sciences of the United States of America 118.5(2021).