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Background   Francisella tularensis  is an intracellular pathogen that causes tularemia in humans and the public health importance of this bacterium has been well documented in recent history.  Francisella philomiragia , a distant relative of  F .  tularensis , is thought to constitute an  environmental lineage  along with  Francisella novicida . Nevertheless, both  F .  philomiragia  and  F .  novicida  have been associated with human disease, primarily in immune-compromised individuals. To understand the genetic relationships and evolutionary contexts among different lineages within the genus  Francisella , the genome of  Francisella  spp. strain TX07-7308 was sequenced and compared to the genomes of  F. philomiragia  strains ATCC 25017 and 25015,  F .  novicida  strain U112, and  F .  tularensis  strain Schu S4.    Results  The size of strain ATCC 25017 chromosome was 2,045,775 bp and contained 1,983 protein-coding genes. The size of strain TX07-7308 chromosome was 2,035,931 bp and contained 1,980 protein-coding genes. Pairwise BLAST comparisons indicated that strains TX07-7308 and ATCC 25017 contained 1,700 protein coding genes in common. NUCmer analyses revealed that the chromosomes of strains TX07-7308 and ATCC 25017 were mostly collinear except for a few gaps, translocations, and/or inversions. Using the genome sequence data and comparative analyses with other members of the genus  Francisella  ( e.g. ,  F .  novicida  strain U112 and  F .  tularensis  strain Schu S4), several strain-specific genes were identified. Strains TX07-7308 and ATCC 25017 contained an operon with six open reading frames encoding proteins related to enzymes involved in thiamine biosynthesis that was absent in  F .  novicida  strain U112 and  F .  tularensis  strain Schu S4. Strain ATCC 25017 contained an operon putatively involved in lactose metabolism that was absent in strain TX07-7308,  F .  novicida  strain U112, and  F .  tularensis  strain Schu S4. In contrast, strain TX07-7308 contained an operon putatively involved in glucuronate metabolism that was absent in the genomes of strain ATCC 25017,  F .  novicida  strain U112, and  F .  tularensis  strain Schu S4. The polymorphic nature of polysaccharide biosynthesis/modification gene clusters among different  Francisella  strains was also evident from genome analyses.    Conclusions  From genome comparisons, it appeared that genes encoding novel functions have contributed to the metabolic enrichment of the  environmental lineages  within the genus  Francisella . The inability to acquire new genes coupled with the loss of ancestral traits and the consequent reductive evolution may be a cause for, as well as an effect of, niche selection of  F. tularensis . Sequencing and comparison of the genomes of more isolates are required to obtain further insights into the ecology and evolution of different species within the genus  Francisella .

bmc genomics

Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources