Abstract
BackgroundProkaryotes are asexual, but these organisms frequently engage in homologous recombination, a process that differs from meiotic recombination in sexual organisms. Most tools developed to simulate genome evolution either assume sexual reproduction or the complete absence of DNA flux in the population. As a result, very few simulators are adapted to model prokaryotic genome evolution while accounting for recombination. Moreover, many simulators are based on the coalescent, which assumes a neutral model of genomic evolution, and those are best suited for organisms evolving under weak selective pressures, such as animals and plants. In contrast, prokaryotes are thought to be evolving under much stronger selective pressures, suggesting that forward-in-time simulators are better suited for these organisms.ResultsHere, I present CoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection.ConclusionsCoreSimul is a flexible forward-in-time simulator that constitutes a significant addition to the limited list of available simulators applicable to prokaryote genome evolution.
Highlights
ResultsI present CoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination
Prokaryotes are asexual, but these organisms frequently engage in homologous recombination, a process that differs from meiotic recombination in sexual organisms
Recent analyses are suggesting a prevalent role of homologous recombination in prokaryotes and the vast majority of bacterial species appears to be impacted by this process, indicating that simulation frameworks incorporating homologous recombination are needed [16, 19,20,21]
Summary
I present CoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection
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