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Some (bacilli) like it hot: genomics of Geobacillus species.

Studholme DJ - Microb Biotechnol (2014)

View Article: PubMed Central - PubMed

Affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.

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The genus Geobacillus includes thermophilic Gram-positive spore-forming bacteria that form a phylogenetically coherent clade within the family Bacillaceae... Genome sequences are also available for some other thermophilic members of the Bacillaceae, such as Paenibacillus lautus (Mead et al., ) and Bacillus coagulans (Xu et al., ) and for Geobacillus-infecting bacteriophage (Marks and Hamilton, ), but these will not be discussed here... However, the availability of complete genome sequence data enables phylogenetic analysis based on single-nucleotide variants over the entire core genome, offering much greater resolution (Fig.  3A)... According to the core-genome-wide phylogenetic analysis, the two strains assigned as G.  kaustophilus do not form a phylogenetically coherent monophyletic clade... Nucleotide sequence identities between clades are much lower; between G.  kaustophilus and G.  thermoglucosidans, there is approximately 84% identity... The considerable amount of reticulation in the phylogenetic network (Fig.  3A) suggests significant horizontal genetic transfer within and among these species... CAMR12739... The NG80-2 genome sequence also enabled discovery of the first nitrous oxide reductase gene from a Gram-positive, and a novel thermophilic long-chain alkane monooxygenase (Feng et al., )... Specifically, they used the genome sequence to clone two promoters and incorporated them into plasmid vectors: one for inducible gene expression and one constitutive... The authors also mention that they tried other promoters that did not work so well; presumably, the availability of the genome sequence allowed them to relatively quickly screen a number of candidates until they found the best ones... Only then can we rationally design genetic interventions to predictably manipulate metabolism... And finally, palaeo-genomics of ancient Geobacillus spores, which may be viable after billions of years of dormancy, might shed light on population-genetics and evolutionary processes over timescales that we previously assumed to be intractable (Nicholson, ; Zeigler, ).

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Relationships among sequenced genomes within the G. kaustophilus clade resolved using whole-genome sequence data. The phylogenetic network in panel A was based on a concatenation of 1722 variant single-nucleotide sites in 1 874 967 nucleotides of the core genome present in all 15 genomes. The network was generated using the neighbornetalgorithm (Bryant and Moulton, 2004) implemented in the splitstree software package (Huson, 1998). The heat-map in B indicates the presence (dark blue) and absence (light blue) of each of 931 non-core genes from the genome of G. thermoleovorans CCB US3 UF6 across the same 15 genomes appearing in A. The gene-content clusters are shaded in the same colours in both panels. The heat-map was rendered using Raivo Kolde's pheatmap package in R (R Development Core Team, R, 2013).
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fig03: Relationships among sequenced genomes within the G. kaustophilus clade resolved using whole-genome sequence data. The phylogenetic network in panel A was based on a concatenation of 1722 variant single-nucleotide sites in 1 874 967 nucleotides of the core genome present in all 15 genomes. The network was generated using the neighbornetalgorithm (Bryant and Moulton, 2004) implemented in the splitstree software package (Huson, 1998). The heat-map in B indicates the presence (dark blue) and absence (light blue) of each of 931 non-core genes from the genome of G. thermoleovorans CCB US3 UF6 across the same 15 genomes appearing in A. The gene-content clusters are shaded in the same colours in both panels. The heat-map was rendered using Raivo Kolde's pheatmap package in R (R Development Core Team, R, 2013).

Mentions: The phylogenetic group within Geobacillus most richly represented by genome sequences is the clade containing G. thermoleovorans, G. kaustophilus and G. thermocatenulatus (see the ‘kaustophilus clade’ in Fig. 2). Based solely of sequences of the recN phylogenetic marker, it is not possible to precisely resolve relationships among sequenced strains within this group (Fig. 2). However, the availability of complete genome sequence data enables phylogenetic analysis based on single-nucleotide variants over the entire core genome, offering much greater resolution (Fig. 3A). According to the core-genome-wide phylogenetic analysis, the two strains assigned as G. kaustophilus do not form a phylogenetically coherent monophyletic clade. On the other hand, the two strains of G. thermoleovorans are closely related and share 99.4% nucleotide sequence identity [based on mummer2 alignments (Delcher et al., 2002)]. Strain FW23 also appears to fall within this clade and, subject to phenotypic characterization, can probably be considered a member of this species too. Geobacillus thermocatenulatus GS-1 is much more divergent, sharing only 94% to 95% identity with the other strains in the clade, which is consistent with the recN-based analysis (Fig. 2). Strains Y412MC52 and YP412MC61 appear to be extremely closely related to each other, sharing 99.8% sequence identity and showing no detectable differences in gene content. Nucleotide sequence identities between clades are much lower; between G. kaustophilus and G. thermoglucosidans, there is approximately 84% identity.


Some (bacilli) like it hot: genomics of Geobacillus species.

Studholme DJ - Microb Biotechnol (2014)

Relationships among sequenced genomes within the G. kaustophilus clade resolved using whole-genome sequence data. The phylogenetic network in panel A was based on a concatenation of 1722 variant single-nucleotide sites in 1 874 967 nucleotides of the core genome present in all 15 genomes. The network was generated using the neighbornetalgorithm (Bryant and Moulton, 2004) implemented in the splitstree software package (Huson, 1998). The heat-map in B indicates the presence (dark blue) and absence (light blue) of each of 931 non-core genes from the genome of G. thermoleovorans CCB US3 UF6 across the same 15 genomes appearing in A. The gene-content clusters are shaded in the same colours in both panels. The heat-map was rendered using Raivo Kolde's pheatmap package in R (R Development Core Team, R, 2013).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321371&req=5

fig03: Relationships among sequenced genomes within the G. kaustophilus clade resolved using whole-genome sequence data. The phylogenetic network in panel A was based on a concatenation of 1722 variant single-nucleotide sites in 1 874 967 nucleotides of the core genome present in all 15 genomes. The network was generated using the neighbornetalgorithm (Bryant and Moulton, 2004) implemented in the splitstree software package (Huson, 1998). The heat-map in B indicates the presence (dark blue) and absence (light blue) of each of 931 non-core genes from the genome of G. thermoleovorans CCB US3 UF6 across the same 15 genomes appearing in A. The gene-content clusters are shaded in the same colours in both panels. The heat-map was rendered using Raivo Kolde's pheatmap package in R (R Development Core Team, R, 2013).
Mentions: The phylogenetic group within Geobacillus most richly represented by genome sequences is the clade containing G. thermoleovorans, G. kaustophilus and G. thermocatenulatus (see the ‘kaustophilus clade’ in Fig. 2). Based solely of sequences of the recN phylogenetic marker, it is not possible to precisely resolve relationships among sequenced strains within this group (Fig. 2). However, the availability of complete genome sequence data enables phylogenetic analysis based on single-nucleotide variants over the entire core genome, offering much greater resolution (Fig. 3A). According to the core-genome-wide phylogenetic analysis, the two strains assigned as G. kaustophilus do not form a phylogenetically coherent monophyletic clade. On the other hand, the two strains of G. thermoleovorans are closely related and share 99.4% nucleotide sequence identity [based on mummer2 alignments (Delcher et al., 2002)]. Strain FW23 also appears to fall within this clade and, subject to phenotypic characterization, can probably be considered a member of this species too. Geobacillus thermocatenulatus GS-1 is much more divergent, sharing only 94% to 95% identity with the other strains in the clade, which is consistent with the recN-based analysis (Fig. 2). Strains Y412MC52 and YP412MC61 appear to be extremely closely related to each other, sharing 99.8% sequence identity and showing no detectable differences in gene content. Nucleotide sequence identities between clades are much lower; between G. kaustophilus and G. thermoglucosidans, there is approximately 84% identity.

View Article: PubMed Central - PubMed

Affiliation: Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

The genus Geobacillus includes thermophilic Gram-positive spore-forming bacteria that form a phylogenetically coherent clade within the family Bacillaceae... Genome sequences are also available for some other thermophilic members of the Bacillaceae, such as Paenibacillus lautus (Mead et al., ) and Bacillus coagulans (Xu et al., ) and for Geobacillus-infecting bacteriophage (Marks and Hamilton, ), but these will not be discussed here... However, the availability of complete genome sequence data enables phylogenetic analysis based on single-nucleotide variants over the entire core genome, offering much greater resolution (Fig.  3A)... According to the core-genome-wide phylogenetic analysis, the two strains assigned as G.  kaustophilus do not form a phylogenetically coherent monophyletic clade... Nucleotide sequence identities between clades are much lower; between G.  kaustophilus and G.  thermoglucosidans, there is approximately 84% identity... The considerable amount of reticulation in the phylogenetic network (Fig.  3A) suggests significant horizontal genetic transfer within and among these species... CAMR12739... The NG80-2 genome sequence also enabled discovery of the first nitrous oxide reductase gene from a Gram-positive, and a novel thermophilic long-chain alkane monooxygenase (Feng et al., )... Specifically, they used the genome sequence to clone two promoters and incorporated them into plasmid vectors: one for inducible gene expression and one constitutive... The authors also mention that they tried other promoters that did not work so well; presumably, the availability of the genome sequence allowed them to relatively quickly screen a number of candidates until they found the best ones... Only then can we rationally design genetic interventions to predictably manipulate metabolism... And finally, palaeo-genomics of ancient Geobacillus spores, which may be viable after billions of years of dormancy, might shed light on population-genetics and evolutionary processes over timescales that we previously assumed to be intractable (Nicholson, ; Zeigler, ).

Show MeSH
Related in: MedlinePlus