首页> 外文期刊>Genome Biology and Evolution >Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution
【24h】

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

机译:Oryza基因组中的古代内源性副逆转录病毒为病毒基因宏进化的异质性提供了见识。

获取原文
           

摘要

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?×?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.
机译:真核生物基因组中的内源性病毒序列,例如来源于植物副逆转录病毒(PRV)的序列,可以作为研究病毒宏进化的基因组化石。病毒进化率的许多方面是异质的,包括基因之间的替代率差异。但是,这种病毒基因速率异质性(GRH)的进化动力学很少被检查。表征此类GRH可能有助于阐明病毒适应性进化。在这项研究中,基于可靠的系统发育分析,我们确定了Oryza基因组中一个古老的内源PRV组,范围为2.41-15.00?Myr。随后,我们使用了这个古老的内生PRV组和三个年轻的组来估计PRV的GRH。最保守的基因和趋异基因的长期替代率为2.69××10×8至8.07××10×8和4.72××10×8至1.42××10×7替换/位点/一年。在直接比较的基础上,这两个基因之间的长期GRH为1.83倍,这出乎意料地低于和低于使用已公开数据计算的PRV的短期GRH(> 3.40倍)。 PRV的长期GRH较低是由于进化过程中发散基因比保守基因的衰变速率稍快。据我们所知,我们首次使用古病毒学分析对病毒基因的长期GRH进行了量化,并提出PRV的GRH在时间尺度上可能是异质的(时间依赖性GRH)。我们的发现为病毒基因的宏观进化提供了特殊的见识,并应鼓励对病毒GRH进行更详细的检查。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱:kefu@zhangqiaokeyan.com

京公网安备:11010802029741号 ICP备案号:京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有
  • 客服微信

  • 服务号