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Background  The genus  Streptococcus  comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple  Streptococcus  strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of  Streptococcus suis , 50 strains of  Streptococcus pyogenes  and 28 strains of  Streptococcus pneumoniae .    Results  Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.  The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.  Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in  S. pneumoniae  leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.    Conclusions  Members of genus  Streptococcus  have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.    Electronic supplementary material  The online version of this article (10.1186/s12862-019-1403-6) contains supplementary material, which is available to authorized users.

Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow