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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

Similarities between leuS-infered (A) and whole genome-based (B) tree topologies of 15 publicly available Pantoea, Erwinia, and Pectobacterium genomes. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity of leuS-based tree topology to that from whole genomes. Sulfolobus acidophilus Ron12 I (NC_020247) was used as outgroup.
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Related In: Results  -  Collection


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f5-ebo-10-2014-115: Similarities between leuS-infered (A) and whole genome-based (B) tree topologies of 15 publicly available Pantoea, Erwinia, and Pectobacterium genomes. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity of leuS-based tree topology to that from whole genomes. Sulfolobus acidophilus Ron12 I (NC_020247) was used as outgroup.

Mentions: The tree topologies based on leuS and that derived from 15 complete genomes of Pantoea, Erwinia, and Pectobacterium showed highly similar clustering patterns (Fig. 5). Three clusters representing the different genera were apparent (Fig. 5). The leuS-derived tree topology (Fig. 5A) was 94.0% identical to that of genome-based phylogeny (Fig. 5B). In the leuS tree topology, the edge bifurcating to Pectobacterium carotovorum PC1 and P. carotovorum PCC21 seems to differ from the corresponding edge on the genome-based tree. On the genome-based tree topology, these two strains branched independently (Fig. 5B). A low similarity (73.8%) was observed between leuS-derived tree topology and that of a tree derived from the corresponding 40 complete genomes of 15 distantly related genera of the Enterobactericeae (data not shown).


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)

Similarities between leuS-infered (A) and whole genome-based (B) tree topologies of 15 publicly available Pantoea, Erwinia, and Pectobacterium genomes. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity of leuS-based tree topology to that from whole genomes. Sulfolobus acidophilus Ron12 I (NC_020247) was used as outgroup.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5-ebo-10-2014-115: Similarities between leuS-infered (A) and whole genome-based (B) tree topologies of 15 publicly available Pantoea, Erwinia, and Pectobacterium genomes. Taxa and tree edges, and numbers in color denote differences, and percent edge similarity of leuS-based tree topology to that from whole genomes. Sulfolobus acidophilus Ron12 I (NC_020247) was used as outgroup.
Mentions: The tree topologies based on leuS and that derived from 15 complete genomes of Pantoea, Erwinia, and Pectobacterium showed highly similar clustering patterns (Fig. 5). Three clusters representing the different genera were apparent (Fig. 5). The leuS-derived tree topology (Fig. 5A) was 94.0% identical to that of genome-based phylogeny (Fig. 5B). In the leuS tree topology, the edge bifurcating to Pectobacterium carotovorum PC1 and P. carotovorum PCC21 seems to differ from the corresponding edge on the genome-based tree. On the genome-based tree topology, these two strains branched independently (Fig. 5B). A low similarity (73.8%) was observed between leuS-derived tree topology and that of a tree derived from the corresponding 40 complete genomes of 15 distantly related genera of the Enterobactericeae (data not shown).

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