Genome streamlining: effect of mutation rate and population size on genome size reduction

Genome streamlining, i.e . genome size reduction, is observed in bacteria with very different life traits, including endosymbiotic bacteria and several marine bacteria, raising the question of its evolutionary origin. None of the hypotheses proposed in the literature is firmly established, mainly due to the many confounding factors related to the diverse habitats of species with streamlined genomes. Computational models may help overcome these difficulties and rigor-ously test hypotheses. In this work, we used Aevol, a platform designed to study the evolution of genome architecture, to test two main hypotheses: that an increase in population size ( N ) or mutation rate ( µ ) could cause genome reduction. Pre-evolved individuals were transferred into new conditions, characterized by an increase in population size or mutation rate. In our experiments, both conditions lead to streamlining. However, they lead to very different genome structures. Under increased population size, genomes loose a significant fraction of non-coding sequences, but maintain their coding size, resulting in densely packed genomes (akin to stream-lined marine bacteria genomes). By contrast, under increased mutation rate, genomes loose coding and non-coding sequences (akin to endosymbiotic bacteria genomes). Hence, both factors lead to an overall reduction in genome size, but the coding density of the genome appears to be determined by N × µ . Thus, a broad range of genome size and density can be achieved by different combinations of N and µ . Our results suggest that genome size and coding density are determined by the interplay between selection for phenotypic adaptation and selection for robustness.