TY - JOUR
T1 - Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome
AU - Kojima, Shohei
AU - Yoshikawa, Kohei
AU - Ito, Jumpei
AU - Nakagawa, So
AU - Parrish, Nicholas F.
AU - Horie, Masayuki
AU - Kawano, Shuichi
AU - Tomonaga, Keizo
N1 - Publisher Copyright:
© 2020 Proceedings of the National Academy of Sciences of the United States of America. All rights reserved.
PY - 2021/2/2
Y1 - 2021/2/2
N2 - 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.
AB - 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.
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U2 - 10.1073/pnas.2010758118
DO - 10.1073/pnas.2010758118
M3 - Article
C2 - 33495343
AN - SCOPUS:85100066198
SN - 0027-8424
VL - 118
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 5
M1 - e2010758118
ER -