Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome
- 25 January 2021
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 118 (5)
- https://doi.org/10.1073/pnas.2010758118
Abstract
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.Funding Information
- MEXT | Japan Society for the Promotion of Science (JP20H05682, JP16H06430)
- Japan Agency for Medical Research and Development (JP19fm0208014)
This publication has 35 references indexed in Scilit:
- Endogenous viruses: insights into viral evolution and impact on host biologyNature Reviews Genetics, 2012
- Repetitive Elements May Comprise Over Two-Thirds of the Human GenomePLoS Genetics, 2011
- Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farmsAnnals of Operations Research, 2011
- Endogenous Viral Elements in Animal GenomesPLoS Genetics, 2010
- Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate GenomesPLoS Pathogens, 2010
- Filoviruses are ancient and integrated into mammalian genomesBMC Evolutionary Biology, 2010
- Endogenous non-retroviral RNA virus elements in mammalian genomesNature, 2010
- Viroid Replication: Rolling-Circles, Enzymes and RibozymesViruses, 2009
- Characterization of Adeno-Associated Virus Genomes Isolated from Human TissuesJournal of Virology, 2005
- Capture of retrotransposon DNA at the sites of chromosomal double-strand breaksNature, 1996