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An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea.

Tambong JT, Xu R, Kaneza CA, Nshogozabahizi JC - Evol. Bioinform. Online (2014)

Bottom Line: All genes used in this study were effective at species-level delineation, but the internal nodes represented conflicting common ancestors in fusA- and pyrG-based phylogenies.Pairwise comparison of topological distances and percent similarities indicated a significant differential influence of individual genes on the concatenated tree topology. leuS- and fusA-inferred phylogenies exhibited, respectively, the lowest (4) and highest (52) topological distances to the concatenated tree.We conclude that the concatenated tree topology is strongly influenced by the gene with the highest number of polymorphic and non-synonymous sites in the absence of significant recombination events.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bacteriology, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada.

ABSTRACT
Partial sequences of six core genes (fusA, gyrB, leuS, pyrG, rlpB, and rpoB) of 37 strains of Pantoea species were analyzed in order to obtain a comprehensive view regarding the phylogenetic relationships within the Pantoea genus and compare tree topologies to identify gene(s) for reliable species and subspecies differentiation. All genes used in this study were effective at species-level delineation, but the internal nodes represented conflicting common ancestors in fusA- and pyrG-based phylogenies. Concatenated gene phylogeny gave the expected DNA relatedness, underscoring the significance of a multilocus sequence analysis. Pairwise comparison of topological distances and percent similarities indicated a significant differential influence of individual genes on the concatenated tree topology. leuS- and fusA-inferred phylogenies exhibited, respectively, the lowest (4) and highest (52) topological distances to the concatenated tree. These correlated well with high (96.3%) and low (64.4%) percent similarities of leuS- and fusA-inferred tree topologies to the concatenated tree, respectively. We conclude that the concatenated tree topology is strongly influenced by the gene with the highest number of polymorphic and non-synonymous sites in the absence of significant recombination events.

No MeSH data available.


Related in: MedlinePlus

Genomic location of core housekeeping genes used in this study based on P. ananatis LMG 5342 (Genbank genome accession number HE617160.1).
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Related In: Results  -  Collection


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f1-ebo-10-2014-115: Genomic location of core housekeeping genes used in this study based on P. ananatis LMG 5342 (Genbank genome accession number HE617160.1).

Mentions: The selected genes (leuS, rpoB, gyrB, fusA, pyrG, and rplB) were previously reported by Delétoile et al.1 in a study of P. agglomerans strains because of its opportunistic pathogen status in humans. Figure 1 shows the genomic location of the genes used in this study based on P. ananatis LMG 5342 (HE617160.1). These are single copy genes in most bacterial genera with important functional roles. leuS encodes leucyl-tRNA synthetase involved in translation. pyrG is implicated in glutamine hydrolysis through CTP synthase; rpoB encodes for the β subunit of RNA polymerase; gyrB is the structural gene for the DNA gyrase β subunit; and fusA encodes the protein synthesis elongation factor-G. The primers reported by Delétoile et al.1 were designed from conserved regions.


An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea.

Tambong JT, Xu R, Kaneza CA, Nshogozabahizi JC - Evol. Bioinform. Online (2014)

Genomic location of core housekeeping genes used in this study based on P. ananatis LMG 5342 (Genbank genome accession number HE617160.1).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4125426&req=5

f1-ebo-10-2014-115: Genomic location of core housekeeping genes used in this study based on P. ananatis LMG 5342 (Genbank genome accession number HE617160.1).
Mentions: The selected genes (leuS, rpoB, gyrB, fusA, pyrG, and rplB) were previously reported by Delétoile et al.1 in a study of P. agglomerans strains because of its opportunistic pathogen status in humans. Figure 1 shows the genomic location of the genes used in this study based on P. ananatis LMG 5342 (HE617160.1). These are single copy genes in most bacterial genera with important functional roles. leuS encodes leucyl-tRNA synthetase involved in translation. pyrG is implicated in glutamine hydrolysis through CTP synthase; rpoB encodes for the β subunit of RNA polymerase; gyrB is the structural gene for the DNA gyrase β subunit; and fusA encodes the protein synthesis elongation factor-G. The primers reported by Delétoile et al.1 were designed from conserved regions.

Bottom Line: All genes used in this study were effective at species-level delineation, but the internal nodes represented conflicting common ancestors in fusA- and pyrG-based phylogenies.Pairwise comparison of topological distances and percent similarities indicated a significant differential influence of individual genes on the concatenated tree topology. leuS- and fusA-inferred phylogenies exhibited, respectively, the lowest (4) and highest (52) topological distances to the concatenated tree.We conclude that the concatenated tree topology is strongly influenced by the gene with the highest number of polymorphic and non-synonymous sites in the absence of significant recombination events.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bacteriology, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada.

ABSTRACT
Partial sequences of six core genes (fusA, gyrB, leuS, pyrG, rlpB, and rpoB) of 37 strains of Pantoea species were analyzed in order to obtain a comprehensive view regarding the phylogenetic relationships within the Pantoea genus and compare tree topologies to identify gene(s) for reliable species and subspecies differentiation. All genes used in this study were effective at species-level delineation, but the internal nodes represented conflicting common ancestors in fusA- and pyrG-based phylogenies. Concatenated gene phylogeny gave the expected DNA relatedness, underscoring the significance of a multilocus sequence analysis. Pairwise comparison of topological distances and percent similarities indicated a significant differential influence of individual genes on the concatenated tree topology. leuS- and fusA-inferred phylogenies exhibited, respectively, the lowest (4) and highest (52) topological distances to the concatenated tree. These correlated well with high (96.3%) and low (64.4%) percent similarities of leuS- and fusA-inferred tree topologies to the concatenated tree, respectively. We conclude that the concatenated tree topology is strongly influenced by the gene with the highest number of polymorphic and non-synonymous sites in the absence of significant recombination events.

No MeSH data available.


Related in: MedlinePlus