Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution
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 evol...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2018
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| Online Access: | https://hdl.handle.net/10568/164802 |
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| author | Chen, Sunlu Saito, Nozomi Encabo, Jaymee R. Yamada, Kanae Choi, Il-Ryong Kishima, Yuji |
| author_browse | Chen, Sunlu Choi, Il-Ryong Encabo, Jaymee R. Kishima, Yuji Saito, Nozomi Yamada, Kanae |
| author_facet | Chen, Sunlu Saito, Nozomi Encabo, Jaymee R. Yamada, Kanae Choi, Il-Ryong Kishima, Yuji |
| author_sort | Chen, Sunlu |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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 million years 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 × 10−8 to 8.07 × 10−8 and 4.72 × 10−8 to 1.42 × 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 |
| format | Journal Article |
| id | CGSpace164802 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1648022025-05-14T10:24:32Z Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution Chen, Sunlu Saito, Nozomi Encabo, Jaymee R. Yamada, Kanae Choi, Il-Ryong Kishima, Yuji evolution genes genomes pathogens phylogeny plant diseases plant pathogens plant viruses wild relatives 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 million years 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 × 10−8 to 8.07 × 10−8 and 4.72 × 10−8 to 1.42 × 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 2018-09-18 2024-12-19T12:54:19Z 2024-12-19T12:54:19Z Journal Article https://hdl.handle.net/10568/164802 en Open Access Oxford University Press Chen, Sunlu; Saito, Nozomi; Encabo, Jaymee R; Yamada, Kanae; Choi, Il-Ryong and Kishima, Yuji. 2018. Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution. Genome Biology and Evolution, (e-first copy); evy207 (34 pages). |
| spellingShingle | evolution genes genomes pathogens phylogeny plant diseases plant pathogens plant viruses wild relatives Chen, Sunlu Saito, Nozomi Encabo, Jaymee R. Yamada, Kanae Choi, Il-Ryong Kishima, Yuji Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution |
| title | Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution |
| title_full | Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution |
| title_fullStr | Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution |
| title_full_unstemmed | Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution |
| title_short | Ancient endogenous pararetroviruses in Oryza genomes provide insights into the heterogeneity of viral gene macroevolution |
| title_sort | ancient endogenous pararetroviruses in oryza genomes provide insights into the heterogeneity of viral gene macroevolution |
| topic | evolution genes genomes pathogens phylogeny plant diseases plant pathogens plant viruses wild relatives |
| url | https://hdl.handle.net/10568/164802 |
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