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Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution

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Title: Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution
Authors: Chen, Sunlu Browse this author
Saito, Nozomi Browse this author →KAKEN DB
Encabo, Jaymee R. Browse this author
Yamada, Kanae Browse this author
Choi, Il-Ryong Browse this author
Kishima, Yuji Browse this author →KAKEN DB
Keywords: genomic fossil
endogenous pararetrovirus
viral gene macroevolution
rate heterogeneity
Issue Date: Oct-2018
Publisher: Oxford University Press
Journal Title: Genome biology and evolution
Volume: 10
Issue: 10
Start Page: 2686
End Page: 2696
Publisher DOI: 10.1093/gbe/evy207
Abstract: Endogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41-15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 x 10(-8) to 8.07 x 10(-8) and 4.72 x 10(-8) to 1.42 x 10(-7) substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.
Rights: © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution., This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Type: article
Appears in Collections:農学院・農学研究院 (Graduate School of Agriculture / Faculty of Agriculture) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 貴島 祐治

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