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. 2018 Nov 19;8:17009. doi: 10.1038/s41598-018-35300-y

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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(A) Phylogenetic tree showing the relationship of the sequenced Bacillus spp. strains. The Bacillus strains included six B. subtilis (BSn5, SG-6, XF-1, BAB-1, BSD-2, and HJ5) and six B. amyloliquefaciens strains (CAUB946, SQR9, UCMB5113, CC178, FZB42, and UCMB5036) and two B. pumilus strains (WP8 and INR7) and four B. cereus strains(905, AR156, UW85, and LCR12). The tree is based on the 607 single-copy core genes and was generated using RAxML 8.2.10. P. polymyxa M1 was used as the out-group. Percent bootstrap values (from 100 replicates) are indicated at the nodes. (B) Genomic diversity of B. cereus strains. Each strain is represented by an oval. The number of orthologous protein-coding genes shared by all strains (the core genome) is at the center. Overlapping regions show the number of CDS represented by several strains. Numbers in nonoverlapping portions of each oval show the number of CDS unique to each strain. The total number of protein-coding genes within each genome is listed below the strain name. (C) Function classification of strain-specific genes in the four B. cereus strains. Comparison was based on 22 COGs categories: energy production and conversion (C); cell cycle control, cell division, and chromosome partitioning (D); amino acid transport and metabolism (E); nucleotide transport and metabolism (F); carbohydrate transport and metabolism (G); coenzyme transport and metabolism (H); lipid transport and metabolism (I); translation, ribosomal structure, and biogenesis (J); transcription (K); replication, recombination, and repair (L); cell wall, membrane, and envelope biogenesis (M); cell motility (N); posttranslational modification, protein turnover, and chaperones (O); inorganic transport and metabolism (P); secondary metabolites biosynthesis, transport, and catabolism (Q); general function prediction only (R); function unknown (S); signal transduction mechanisms (T); intracellular trafficking, secretion, and vesicular transport (U); and defense mechanisms (V).