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KMID : 0364820200560030254
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Korean Journal of Microbiology
2020 Volume.56 No. 3 p.254 ~ p.268
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An analysis of homologous recombination of African swine fever virus using a model-based phylogenetic approach
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Choi Sang-Chul
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Abstract
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Homologous recombination and point mutations are known to affect African swine fever (ASF) virus evolution. Here, the relative effects of these two evolutionary forces are quantified via the model-based ClonalFrameML approach that is often employed for analyzing bacterial genomes but that is also applicable to the ASF virus due to its long genome. Using recombinant genome regions that were inferred after aligning ASF virus genomes, we found that the substitution effect of recombination in the ASF virus genome analysis was about one and a half times that of point mutation. We also carefully compare ASF virus phylogenies that are estimated when considering and when ignoring recombination. We determine that failure to incorporate recombination into inference of ASF virus trees results in large distortions of estimated branch lengths. We conclude by discussing the prospects of applying the ClonalFrameML framework in order to study the evolution of other viruses with long genomes.
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KEYWORD
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ASF virus, gene set enrichment, genetic variation, maximum-likelihood, phylogenetics
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