| Summary: | <p>Abstract</p> <p>Background</p> <p>The presence of <it>Bacillus </it>in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known <it>Bacillus</it>.</p> <p>Results</p> <p>Our analysis is based upon twenty complete and draft <it>Bacillus </it>genomes, including a newly sequenced <it>Bacillus </it>isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known <it>Bacilli</it>, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced <it>Bacillus</it>, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of <it>Bacillus</it>, such as sporulation and competence, and showed that less than one third of the <it>B. subtilis </it>genes are conserved across other <it>Bacilli</it>. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that <it>Bacilli </it>have genetically specialized to allow for the occupation of diverse habitats and niches.</p> <p>Conclusions</p> <p>The aquatic <it>Bacilli </it>are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the <it>Bacilli </it>was unexpected based on previous studies of the <it>B. subtilis </it>model alone. The challenge of uncovering the novelties and variations among genes of the non-<it>subtilis </it>groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches.</p>
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