The discovery of the diversity of the gene repertoires, even among bacteria and archaea with closely related nucleotide sequences, led to a conceptual shift in microbiology. Taken together, these findings have inspired the concept of genome reduction as the `default' evolutionary process counterbalanced by episodes of gene gain, primarily via HGT. Furthermore, gene loss has been reported to be a more uniform, `clock-like' process than gene gain, which shows a stronger episodic character. These findings are compatible with the observation of the overall deletion bias in the evolution of prokaryotic (as well as eukaryotic) genomes. However, genome reduction, often described as streamlining, also prevails in the evolution of bacterial saprophytes, and some free-living microbes, particularly in marine environments. In obligate intracellular parasitic bacteria as well as in parasitic archaea, gene loss is the single dominant evolutionary process ,. Averaged over long spans of evolution, gene loss appears to be a more common process than gene gain as shown for different groups of bacteria and archaea ,. All evolutionary reconstructions performed with widely different groups of bacteria and archaea infer various combinations of vertical inheritance, gene loss and gain. These approaches typically employ the pattern of gene presence/absence in a set of species, which is mapped onto a guide phylogenetic tree. Beyond the comparative genomic observations, estimates of the genome dynamics rates in prokaryotes have been obtained via explicit evolutionary reconstruction using maximum parsimony or maximum likelihood (ML) methods. The enormous diversity of the gene repertoires among bacteria and archaea implies that prokaryotic genomes exist in a state of incessant flux, expanding through horizontal gene transfer (HGT), gene duplication and possibly de novo emergence of genes, and contracting via gene loss ,. Substantial differences in genome size and gene content are often evident between species within the same genus - and even between strains of the same species. This broad range of genome sizes is reflected in the diversity of gene repertoires: only a tiny minority of prokaryotic genes are (nearly) universal whereas the great majority are present in small subsets of genomes. Prokaryotic genomes present a wide variety of genome sizes, from approximately 150 kb in some intracellular endosymbionts of insects to approximately 13 Mb in the largest cyanobacteria and myxobacteria. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.Ĭomparative genomics of bacteria and archaea (collectively, prokaryotes) reveals extensive variation of gene repertoires, which is thought to reflect a highly dynamic regime of genome evolution. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, `open' supergenomes. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. pools of genes that are accessible to the given microbial species. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss.