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Background  Prior to this study, relatively few strains of  Francisella  had been genome-sequenced. Previously published  Francisella  genome sequences were largely restricted to the zoonotic agent  F. tularensis . Only limited data were available for other members of the  Francisella  genus, including  F. philomiragia , an opportunistic pathogen of humans,  F. noatunensis,  a serious pathogen of farmed fish, and other less well described endosymbiotic species.    Results  We determined the phylogenetic relationships of all known  Francisella  species, including some for which the phylogenetic positions were previously uncertain. The genus  Francisella  could be divided into two main genetic clades: one included  F. tularensis, F. novicida, F. hispaniensis  and  Wolbachia persica , and another included  F. philomiragia  and  F. noatunensis .  Some  Francisella  species were found to have significant recombination frequencies. However, the fish pathogen  F. noatunensis  subsp.  noatunensis  was an exception due to it exhibiting a highly clonal population structure similar to the human pathogen  F. tularensis.Conclusions  The genus  Francisella  can be divided into two main genetic clades occupying both terrestrial and marine habitats. However, our analyses suggest that the ancestral  Francisella  species originated in a marine habitat. The observed genome to genome variation in gene content and IS elements of different species supports the view that similar evolutionary paths of host adaptation developed independently in  F. tularensis  (infecting mammals) and  F. noatunensis  subsp.  noatunensis  (infecting fish).

Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish