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Background  Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the  Planctomyctetes, Verrumicrobia, Chlamydiae  (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan.    Results  Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome’s content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with  Proteobacteria , and bacteria from vertebrates, which exchanged more with  Firmicutes . The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats.    Conclusions  The presence of an intracytoplasmic membrane in PVC species seems to affect the genome’s evolution through the selection of transferred DNA, according to their encoded functions.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-017-0921-3) contains supplementary material, which is available to authorized users.

Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum