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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

Least square tendency lines identified leuS as the most discriminating gene by correlation of phylogenetic distances between Pantoea strains as indicated by Mulet et al.19
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Related In: Results  -  Collection


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f2-ebo-10-2014-115: Least square tendency lines identified leuS as the most discriminating gene by correlation of phylogenetic distances between Pantoea strains as indicated by Mulet et al.19

Mentions: The six genes were compared in order to determine the most discriminating gene or genes. A matrix of the phylogenetic distances between all the 37 strains was constructed for each single gene and the distances (3996 values) of pairs of strains were plotted.19 Plots were generated between leuS (exhibiting the highest number of polymorphic sites) or rlpB (lowest polymorphic sites) and the other five core genes. The ratio between the leuS slope and the slopes of the other genes was calculated as a measure of the discriminating potential of each gene19: leuS/rlpB (3.75 times); leuS/pyrG (1.88 times); leuS/rpoB (1.88 times); leuS/fusA (1.55 times); leuS/gyrB (1.25 times). The slopes of least square tendency lines indicate that Pantoea strains have the most distinguished genetic distance for one another in gene leuS, and to suggest that leuS is the most discriminating gene, which is followed by gyrB. Similarly, the matrix constructed for the concatenated nucleotide sequences of the six protein-coding genes (2997nt) was compared in a pairwise manner to assess the correlation and the relative discriminatory power (Fig. 2). The matrix distance of the concatenated sequence least correlated with rlpB, while maximum correlations were obtained with leuS and gyrB (Fig. 2). leuS and gyrB were 50 and 20% more discriminatory than the concatenated gene sequences, while fusA was comparable to that of the concatenated sequence. rpoB, pyrG, and rlpB were less discriminatory (Fig. 2) than the concatenated sequences.


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)

Least square tendency lines identified leuS as the most discriminating gene by correlation of phylogenetic distances between Pantoea strains as indicated by Mulet et al.19
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2-ebo-10-2014-115: Least square tendency lines identified leuS as the most discriminating gene by correlation of phylogenetic distances between Pantoea strains as indicated by Mulet et al.19
Mentions: The six genes were compared in order to determine the most discriminating gene or genes. A matrix of the phylogenetic distances between all the 37 strains was constructed for each single gene and the distances (3996 values) of pairs of strains were plotted.19 Plots were generated between leuS (exhibiting the highest number of polymorphic sites) or rlpB (lowest polymorphic sites) and the other five core genes. The ratio between the leuS slope and the slopes of the other genes was calculated as a measure of the discriminating potential of each gene19: leuS/rlpB (3.75 times); leuS/pyrG (1.88 times); leuS/rpoB (1.88 times); leuS/fusA (1.55 times); leuS/gyrB (1.25 times). The slopes of least square tendency lines indicate that Pantoea strains have the most distinguished genetic distance for one another in gene leuS, and to suggest that leuS is the most discriminating gene, which is followed by gyrB. Similarly, the matrix constructed for the concatenated nucleotide sequences of the six protein-coding genes (2997nt) was compared in a pairwise manner to assess the correlation and the relative discriminatory power (Fig. 2). The matrix distance of the concatenated sequence least correlated with rlpB, while maximum correlations were obtained with leuS and gyrB (Fig. 2). leuS and gyrB were 50 and 20% more discriminatory than the concatenated gene sequences, while fusA was comparable to that of the concatenated sequence. rpoB, pyrG, and rlpB were less discriminatory (Fig. 2) than the concatenated sequences.

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