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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.


Neighbor-joining tree constructed based on the sequences of the 16S rRNA gene from 50 Bacillus strains.Escherichia coli Bl21 (DE3) (AM946981.2) 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; Green Square for Bacillus subtilis.
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f7: Neighbor-joining tree constructed based on the sequences of the 16S rRNA gene from 50 Bacillus strains.Escherichia coli Bl21 (DE3) (AM946981.2) 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; Green Square for Bacillus subtilis.

Mentions: Three NJ trees inferred from the data of three single genes (16s rRNA gene, GryB and AroE), are shown in Figs 7, 8, 9 respectively. These trees did not support the monophyletic status of B. anthracis. The clades that contain B. anthracis strains also contain other Bacillus species (e.g. B. cereus AH820 in Clade II of Fig. 8, and B. thuringiensis serovar monterrey BGSC 4AJ1 in Clade D of Fig. 9). Among the total 23 B. thuringiensis strains studied, some strains form monophyletic sub - clades in trees inferred from GyrB (Clade V, Fig. 8) and AroE (Clade A and C, Fig. 9), but the monophyletic status of the whole B. thuringiensis strains cannot be confirmed by these analyses. Similarly, B. cereus proved to be a paraphyletic group by all NJ trees inferred from data of three single genes. The data for GyrB and AroE suggested that B. subtilis might be a monophyletic group (Clade IV in Fig. 8 and Clade B in Fig. 9), and this group has close relationship with B. licheniformis DSM 13 ATCC 14580, which is supported by high bootstrap value (97 in Fig. 8 and 99 in Fig. 9). With respect to the phylogenetic placement of B. subtilis and B. licheniformis, the 16S rRNA gene shows very low support in comparison to the other two protein coding genes (Fig. 7).


Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
Neighbor-joining tree constructed based on the sequences of the 16S rRNA gene from 50 Bacillus strains.Escherichia coli Bl21 (DE3) (AM946981.2) 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; Green Square for Bacillus subtilis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f7: Neighbor-joining tree constructed based on the sequences of the 16S rRNA gene from 50 Bacillus strains.Escherichia coli Bl21 (DE3) (AM946981.2) 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; Green Square for Bacillus subtilis.
Mentions: Three NJ trees inferred from the data of three single genes (16s rRNA gene, GryB and AroE), are shown in Figs 7, 8, 9 respectively. These trees did not support the monophyletic status of B. anthracis. The clades that contain B. anthracis strains also contain other Bacillus species (e.g. B. cereus AH820 in Clade II of Fig. 8, and B. thuringiensis serovar monterrey BGSC 4AJ1 in Clade D of Fig. 9). Among the total 23 B. thuringiensis strains studied, some strains form monophyletic sub - clades in trees inferred from GyrB (Clade V, Fig. 8) and AroE (Clade A and C, Fig. 9), but the monophyletic status of the whole B. thuringiensis strains cannot be confirmed by these analyses. Similarly, B. cereus proved to be a paraphyletic group by all NJ trees inferred from data of three single genes. The data for GyrB and AroE suggested that B. subtilis might be a monophyletic group (Clade IV in Fig. 8 and Clade B in Fig. 9), and this group has close relationship with B. licheniformis DSM 13 ATCC 14580, which is supported by high bootstrap value (97 in Fig. 8 and 99 in Fig. 9). With respect to the phylogenetic placement of B. subtilis and B. licheniformis, the 16S rRNA gene shows very low support in comparison to the other two protein coding genes (Fig. 7).

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.