Ancient endogenous pararetroviruses in oryza genomes provide insights into the heterogeneity of viral gene macroevolution

Abstract

© 2018 Oxford University Press. All rights reserved. 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 genewere 2.69108 to 8.07108 and 4.72108 to 1.42107 substitutions/site/year, respectively. On the basis of a direct comparison, a long-termGRHof 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-termGRH 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.

Source or Periodical Title

Genome Biology and Evolution

Page

2686-2696

Document Type

Article

Subject

Endogenous pararetrovirus, Genomic fossil, Oryza., Paleovirology, Rate heterogeneity, Viral gene macroevolution

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