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Open Access Research article

Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group

Timothy R Schmidt, Edgar J Scott and David W Dyer*

Author Affiliations

Department of Microbiology and Immunology, Oklahoma University Health Sciences Center, Oklahoma City, OK 73117 USA

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BMC Genomics 2011, 12:430  doi:10.1186/1471-2164-12-430

Published: 24 August 2011

Additional files

Additional file 1:

Single-copy genes used in the phylogenetic analysis of the Bacillaceae. Annotations for each of the single-copy gene are from the Paenibacillus genome as submitted to Genbank, one of the outgroups included in the analysis.

Format: XLS Size: 27KB Download file

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Open Data

Additional file 2:

Sigma factor genes identified in this study. Locus tags for genes found in each genome follow the locus tag identifier or sigma factor identifier for each ortholog.

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Additional file 3:

Results of MEME analysis of the sigma factor genes identified in iterative BLAST searches. MEME results for 10 motifs (nmotifs = 10) are shown, 7 of which follow phylogenetic patterns that differentiate PA from ECF sigma factors (Tables 2 and 3).

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Additional file 4:

Results of phylogenetic analysis of the sigma factors identified in Additional file 2. Phylogenetic analysis utilized the neighbor-joining algorithm of MEGA (see text).

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Open Data