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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.


NJ tree of 44 Bacillus strains.The tree was constructed using Parsnp and annotated in MEGA 6.0. The NJ algorithm was based on the Core Genome SNP data of the 44 Bacillus strains. Bacillus weihenstephanensis KBAB4 was used as an outgroup in the analysis. The bootstrap confidence values were generated using 1,000 permutations. Different symbols were allocated to represent different species: Blue triangle for Bacillus thuringiensis; Pink diamond for Bacillus cereus; Red circle for Bacillus anthracis. The Genbank file of Bacillus cereus ATCC 14579 (represented as BC14579) was used as reference in the Parsnp analysis.
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f4: NJ tree of 44 Bacillus strains.The tree was constructed using Parsnp and annotated in MEGA 6.0. The NJ algorithm was based on the Core Genome SNP data of the 44 Bacillus strains. Bacillus weihenstephanensis KBAB4 was used as an outgroup in the analysis. The bootstrap confidence values were generated using 1,000 permutations. Different symbols were allocated to represent different species: Blue triangle for Bacillus thuringiensis; Pink diamond for Bacillus cereus; Red circle for Bacillus anthracis. The Genbank file of Bacillus cereus ATCC 14579 (represented as BC14579) was used as reference in the Parsnp analysis.

Mentions: Our effort in using Harvest suite to analyse all the species examined in FFP was not successful. The shared core genome among all the studied taxa was too low (less than 1%) to let the Parsnp program to work. This is because Parsnp is designed for intraspecific alignments and requires >=97% average nucleotide identity among input genomes. The Parsnp started to work when Bacillus species other than the member of Bacillus cereus sensu lato were excluded from the analysis. The final alignment and the resulting NJ tree are presented in Figs 4, 5, 6. The NJ tree distinguished two highly supported clades (100 in bootstrap value): one including all the B. anthracis strains and the other including sixteen B. thuringiensis strains. The whole topology of this NJ tree is highly similar to that of the NJ trees inferred from FFP and kSNP analyses (Figs 1 and 2).


Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
NJ tree of 44 Bacillus strains.The tree was constructed using Parsnp and annotated in MEGA 6.0. The NJ algorithm was based on the Core Genome SNP data of the 44 Bacillus strains. Bacillus weihenstephanensis KBAB4 was used as an outgroup in the analysis. The bootstrap confidence values were generated using 1,000 permutations. Different symbols were allocated to represent different species: Blue triangle for Bacillus thuringiensis; Pink diamond for Bacillus cereus; Red circle for Bacillus anthracis. The Genbank file of Bacillus cereus ATCC 14579 (represented as BC14579) was used as reference in the Parsnp analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: NJ tree of 44 Bacillus strains.The tree was constructed using Parsnp and annotated in MEGA 6.0. The NJ algorithm was based on the Core Genome SNP data of the 44 Bacillus strains. Bacillus weihenstephanensis KBAB4 was used as an outgroup in the analysis. The bootstrap confidence values were generated using 1,000 permutations. Different symbols were allocated to represent different species: Blue triangle for Bacillus thuringiensis; Pink diamond for Bacillus cereus; Red circle for Bacillus anthracis. The Genbank file of Bacillus cereus ATCC 14579 (represented as BC14579) was used as reference in the Parsnp analysis.
Mentions: Our effort in using Harvest suite to analyse all the species examined in FFP was not successful. The shared core genome among all the studied taxa was too low (less than 1%) to let the Parsnp program to work. This is because Parsnp is designed for intraspecific alignments and requires >=97% average nucleotide identity among input genomes. The Parsnp started to work when Bacillus species other than the member of Bacillus cereus sensu lato were excluded from the analysis. The final alignment and the resulting NJ tree are presented in Figs 4, 5, 6. The NJ tree distinguished two highly supported clades (100 in bootstrap value): one including all the B. anthracis strains and the other including sixteen B. thuringiensis strains. The whole topology of this NJ tree is highly similar to that of the NJ trees inferred from FFP and kSNP analyses (Figs 1 and 2).

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.