| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Blochmannia </it>are obligately intracellular bacterial mutualists of ants of the tribe Camponotini. <it>Blochmannia </it>perform key nutritional functions for the host, including synthesis of several essential amino acids. We used Illumina technology to sequence the genome of <it>Blochmannia </it>associated with <it>Camponotus vafer</it>.</p> <p>Results</p> <p>Although <it>Blochmannia vafer </it>retains many nutritional functions, it is missing glutamine synthetase (<it>glnA</it>), a component of the nitrogen recycling pathway encoded by the previously sequenced <it>B. floridanus </it>and <it>B. pennsylvanicus</it>. With the exception of <it>Ureaplasma</it>, <it>B. vafer </it>is the only sequenced bacterium to date that encodes urease but lacks the ability to assimilate ammonia into glutamine or glutamate. Loss of <it>glnA </it>occurred in a deletion hotspot near the putative replication origin. Overall, compared to the likely gene set of their common ancestor, 31 genes are missing or eroded in <it>B. vafer</it>, compared to 28 in <it>B. floridanus </it>and four in <it>B</it>. <it>pennsylvanicus</it>. Three genes (<it>queA, visC </it>and <it>yggS</it>) show convergent loss or erosion, suggesting relaxed selection for their functions. Eight <it>B. vafer </it>genes contain frameshifts in homopolymeric tracts that may be corrected by transcriptional slippage. Two of these encode DNA replication proteins: <it>dnaX</it>, which we infer is also frameshifted in <it>B. floridanus</it>, and <it>dnaG</it>.</p> <p>Conclusions</p> <p>Comparing the <it>B. vafer </it>genome with <it>B. pennsylvanicus </it>and <it>B. floridanus </it>refines the core genes shared within the mutualist group, thereby clarifying functions required across ant host species. This third genome also allows us to track gene loss and erosion in a phylogenetic context to more fully understand processes of genome reduction.</p>
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