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Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)

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ABSTRACT

Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic status of B. anthracis was strongly supported by the analysis. FFP proved to be more effective in inferring the phylogeny of Bacillus than methods based on single gene sequences [16s rRNA gene, GryB (gyrase subunit B) and AroE (shikimate-5-dehydrogenase)] analyses. The findings of FFP analysis were verified using kSNP v2 (alignment-free sequence analysis method) and Harvest suite (core genome sequence alignment method).

No MeSH data available.


Core SNP matrix inferred from kSNP v2 (BA: Bacillus anthracis, BC: Bacillus cereus, BCL: Bacillus clausii, BH: Bacillus halodurans, BL: Bacillus licheniformis, BS: Bacillus subtilis, BT: Bacillus thuringiensis, BW: Bacillus weihenstephanensis).
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f3: Core SNP matrix inferred from kSNP v2 (BA: Bacillus anthracis, BC: Bacillus cereus, BCL: Bacillus clausii, BH: Bacillus halodurans, BL: Bacillus licheniformis, BS: Bacillus subtilis, BT: Bacillus thuringiensis, BW: Bacillus weihenstephanensis).

Mentions: The core SNP matrix resulted from the kSNP analysis provided a direct visualization of the relationships among all the Bacillus species studied (Fig. 3). There was no variation between the core SNPs of B. anthracis and B. thuringiensis, whist only single variation was found for two B. cereus strains (Bacillus cereus AH603 and Bacillus cereus AH621) and B. weihenstephanensis. The variation of core SNP increased to two among the B. subtilis species and the B. licheniformis DSM 13 = ATCC 1458034. The sharp increase of core SNP variations in B. halodurans C-12533 and B. clausii KSM-K16 (4 and 5 respectively) revealed their distant relationships to the remaining Bacillus species.


Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
Core SNP matrix inferred from kSNP v2 (BA: Bacillus anthracis, BC: Bacillus cereus, BCL: Bacillus clausii, BH: Bacillus halodurans, BL: Bacillus licheniformis, BS: Bacillus subtilis, BT: Bacillus thuringiensis, BW: Bacillus weihenstephanensis).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555171&req=5

f3: Core SNP matrix inferred from kSNP v2 (BA: Bacillus anthracis, BC: Bacillus cereus, BCL: Bacillus clausii, BH: Bacillus halodurans, BL: Bacillus licheniformis, BS: Bacillus subtilis, BT: Bacillus thuringiensis, BW: Bacillus weihenstephanensis).
Mentions: The core SNP matrix resulted from the kSNP analysis provided a direct visualization of the relationships among all the Bacillus species studied (Fig. 3). There was no variation between the core SNPs of B. anthracis and B. thuringiensis, whist only single variation was found for two B. cereus strains (Bacillus cereus AH603 and Bacillus cereus AH621) and B. weihenstephanensis. The variation of core SNP increased to two among the B. subtilis species and the B. licheniformis DSM 13 = ATCC 1458034. The sharp increase of core SNP variations in B. halodurans C-12533 and B. clausii KSM-K16 (4 and 5 respectively) revealed their distant relationships to the remaining Bacillus species.

View Article: PubMed Central

ABSTRACT

Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic status of B. anthracis was strongly supported by the analysis. FFP proved to be more effective in inferring the phylogeny of Bacillus than methods based on single gene sequences [16s rRNA gene, GryB (gyrase subunit B) and AroE (shikimate-5-dehydrogenase)] analyses. The findings of FFP analysis were verified using kSNP v2 (alignment-free sequence analysis method) and Harvest suite (core genome sequence alignment method).

No MeSH data available.