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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

Single gene phylogenetic trees inferred by maximum-likelihood (ML) of 37 strains of Pantoea and Tatumella using the general time reversible substitution model. A, leuS; B, gyrB; C, rpoB; D, fusA; E, pyrG; and F, rplB. ML trees were reconstructed for each gene sequences with 1000 bootstrap replicates. Bootstrap values higher than 50 are shown in black on nodes. Tatumella spp. were used as outgroup. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity to that of the concatenated tree.
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f3-ebo-10-2014-115: Single gene phylogenetic trees inferred by maximum-likelihood (ML) of 37 strains of Pantoea and Tatumella using the general time reversible substitution model. A, leuS; B, gyrB; C, rpoB; D, fusA; E, pyrG; and F, rplB. ML trees were reconstructed for each gene sequences with 1000 bootstrap replicates. Bootstrap values higher than 50 are shown in black on nodes. Tatumella spp. were used as outgroup. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity to that of the concatenated tree.

Mentions: Single gene (Fig. 3A–F) and concatenated (Fig. 4) phylogenetic trees from leuS, gyrB, rpoB, fusA, pyrG, and rlpB were computed using ML to determine the phylogenetic relationships between Pantoea species. All single gene trees showed the main lineages (Fig. 3A–F) but some of the internal nodes represented conflicting common ancestors for some species in fusA- and pyrG-based phylogenies. The P. stewartii subgroup regrouped the two described subspecies (subspecies stewartii and indologenes) while the P. ananatis subgroup has all the strains of P. ananatis and Pantoea allii. The P. agglomerans subgroup included strains from P. agglomerans, Pantoea vagans, Pantoea deleyi, and Pantoea eucalypti. However, there were significant differences among genes with respect to the phylogenetic associations of P. dispersa, Pantoea septica, and Pantoea cypripedii. This discrepancy was most evident in fusA phylogeny with these three species sharing a direct ancestor with P. stewartii subgroup (Fig. 3D).


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)

Single gene phylogenetic trees inferred by maximum-likelihood (ML) of 37 strains of Pantoea and Tatumella using the general time reversible substitution model. A, leuS; B, gyrB; C, rpoB; D, fusA; E, pyrG; and F, rplB. ML trees were reconstructed for each gene sequences with 1000 bootstrap replicates. Bootstrap values higher than 50 are shown in black on nodes. Tatumella spp. were used as outgroup. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity to that of the concatenated tree.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3-ebo-10-2014-115: Single gene phylogenetic trees inferred by maximum-likelihood (ML) of 37 strains of Pantoea and Tatumella using the general time reversible substitution model. A, leuS; B, gyrB; C, rpoB; D, fusA; E, pyrG; and F, rplB. ML trees were reconstructed for each gene sequences with 1000 bootstrap replicates. Bootstrap values higher than 50 are shown in black on nodes. Tatumella spp. were used as outgroup. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity to that of the concatenated tree.
Mentions: Single gene (Fig. 3A–F) and concatenated (Fig. 4) phylogenetic trees from leuS, gyrB, rpoB, fusA, pyrG, and rlpB were computed using ML to determine the phylogenetic relationships between Pantoea species. All single gene trees showed the main lineages (Fig. 3A–F) but some of the internal nodes represented conflicting common ancestors for some species in fusA- and pyrG-based phylogenies. The P. stewartii subgroup regrouped the two described subspecies (subspecies stewartii and indologenes) while the P. ananatis subgroup has all the strains of P. ananatis and Pantoea allii. The P. agglomerans subgroup included strains from P. agglomerans, Pantoea vagans, Pantoea deleyi, and Pantoea eucalypti. However, there were significant differences among genes with respect to the phylogenetic associations of P. dispersa, Pantoea septica, and Pantoea cypripedii. This discrepancy was most evident in fusA phylogeny with these three species sharing a direct ancestor with P. stewartii subgroup (Fig. 3D).

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