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Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome
- Source :
- Proc Natl Acad Sci U S A
- Publication Year :
- 2021
- Publisher :
- National Academy of Sciences, 2021.
-
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.
- Subjects :
- Mammals
Multidisciplinary
biology
Base Sequence
Genome, Human
viruses
RNA
RNA virus
Biological Sciences
biology.organism_classification
Genome
Virus
Machine Learning
Mutagenesis, Insertional
Nucleoproteins
Retroviridae
Evolutionary biology
Viral evolution
Animals
Humans
Human genome
Paleovirology
Reference genome
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Proc Natl Acad Sci U S A
- Accession number :
- edsair.doi.dedup.....0ea5b0aad52f1b452c662be89a13f0b5