DNA for Bacillus amyloliquefaciens subsp. amyloliquefaciens DSM7, Deinococcus maricopensis DSM 21211 and Sulfolobus tokodaii DSM 16993, was acquired from the Leibniz-Institut DSMZ – German Collection of Microorganisms and Cell Cultures. These organisms were selected as they had small genomes consisting of a single chromosome, no plasmids, and complete reference genomes. They were also selected to span a range of mean genomic G+C% (B. amyloliquefaciens 46.1%, D. maricopensis 69.8%, S. tokodaii 32.8%). The SFF files for all B. amyloliquefaciens and S. tokodaii datasets are available from http://ecogenomic.org/acacia.