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Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.

Skippington E, Ragan MA - Open Biol (2012)

Bottom Line: Here, we test these hypotheses using a graph-based abstraction of inferred genetic-exchange relationships among 27 Escherichia coli and Shigella genomes.More than one-third of donor-recipient pairs in our analysis show some level of fragmentary gene transfer.Thus, within the E. coli-Shigella clade, intact genes and gene fragments have been disseminated non-uniformly and at appreciable frequency, constructing communities that transgress environmental and lifestyle boundaries.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular Bioscience and Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, Queensland 4072, Australia.

ABSTRACT
Genetic material can be transmitted not only vertically from parent to offspring, but also laterally (horizontally) from one bacterial lineage to another. Lateral genetic transfer is non-uniform; biases in its nature or frequency construct communities of genetic exchange. These biases have been proposed to arise from phylogenetic relatedness, shared ecology and/or common lifestyle. Here, we test these hypotheses using a graph-based abstraction of inferred genetic-exchange relationships among 27 Escherichia coli and Shigella genomes. We show that although barriers to inter-phylogenetic group lateral transfer are low, E. coli and Shigella are more likely to have exchanged genetic material with close relatives. We find little evidence of bias arising from shared environment or lifestyle. More than one-third of donor-recipient pairs in our analysis show some level of fragmentary gene transfer. Thus, within the E. coli-Shigella clade, intact genes and gene fragments have been disseminated non-uniformly and at appreciable frequency, constructing communities that transgress environmental and lifestyle boundaries.

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The E. coli–Shigella reference supertree, constructed using matrix representation with parsimony [38] based on well-supported bipartitions in 5282 Bayesian protein trees. Colours indicate membership in recognized E. coli phylogenetic groups.
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RSOB120112F1: The E. coli–Shigella reference supertree, constructed using matrix representation with parsimony [38] based on well-supported bipartitions in 5282 Bayesian protein trees. Colours indicate membership in recognized E. coli phylogenetic groups.

Mentions: Using whole-genome alignment, we delineated 5282 sets of proteins with at most one member per genome (i.e. putative orthologues) and size n ≥ 4, and for each we inferred a Bayesian phylogenetic tree [37]. Aggregating all well-supported bipartitions (posterior probability, PP ≥ 0.95) using matrix representation with parsimony (MRP) [38] yielded a robust reference topology for E. coli–Shigella (figure 1). This MRP tree is remarkably concordant with the E. coli–Shigella phylogeny reported by Touchon et al. [14], which they inferred by maximum likelihood from 1878 concatenated E. coli–Shigella core gene sequences ([17], fig. 4). Of the 52 bipartitions in our MRP tree, 49 appear in the Touchon et al. tree. Both trees support the monophyly of all classical groups described by multi-locus enzyme electrophoresis [39] except for phylogenetic group D, which both we and Touchon et al. [14] recover as polyphyletic.Figure 1.


Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.

Skippington E, Ragan MA - Open Biol (2012)

The E. coli–Shigella reference supertree, constructed using matrix representation with parsimony [38] based on well-supported bipartitions in 5282 Bayesian protein trees. Colours indicate membership in recognized E. coli phylogenetic groups.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472396&req=5

RSOB120112F1: The E. coli–Shigella reference supertree, constructed using matrix representation with parsimony [38] based on well-supported bipartitions in 5282 Bayesian protein trees. Colours indicate membership in recognized E. coli phylogenetic groups.
Mentions: Using whole-genome alignment, we delineated 5282 sets of proteins with at most one member per genome (i.e. putative orthologues) and size n ≥ 4, and for each we inferred a Bayesian phylogenetic tree [37]. Aggregating all well-supported bipartitions (posterior probability, PP ≥ 0.95) using matrix representation with parsimony (MRP) [38] yielded a robust reference topology for E. coli–Shigella (figure 1). This MRP tree is remarkably concordant with the E. coli–Shigella phylogeny reported by Touchon et al. [14], which they inferred by maximum likelihood from 1878 concatenated E. coli–Shigella core gene sequences ([17], fig. 4). Of the 52 bipartitions in our MRP tree, 49 appear in the Touchon et al. tree. Both trees support the monophyly of all classical groups described by multi-locus enzyme electrophoresis [39] except for phylogenetic group D, which both we and Touchon et al. [14] recover as polyphyletic.Figure 1.

Bottom Line: Here, we test these hypotheses using a graph-based abstraction of inferred genetic-exchange relationships among 27 Escherichia coli and Shigella genomes.More than one-third of donor-recipient pairs in our analysis show some level of fragmentary gene transfer.Thus, within the E. coli-Shigella clade, intact genes and gene fragments have been disseminated non-uniformly and at appreciable frequency, constructing communities that transgress environmental and lifestyle boundaries.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular Bioscience and Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, Queensland 4072, Australia.

ABSTRACT
Genetic material can be transmitted not only vertically from parent to offspring, but also laterally (horizontally) from one bacterial lineage to another. Lateral genetic transfer is non-uniform; biases in its nature or frequency construct communities of genetic exchange. These biases have been proposed to arise from phylogenetic relatedness, shared ecology and/or common lifestyle. Here, we test these hypotheses using a graph-based abstraction of inferred genetic-exchange relationships among 27 Escherichia coli and Shigella genomes. We show that although barriers to inter-phylogenetic group lateral transfer are low, E. coli and Shigella are more likely to have exchanged genetic material with close relatives. We find little evidence of bias arising from shared environment or lifestyle. More than one-third of donor-recipient pairs in our analysis show some level of fragmentary gene transfer. Thus, within the E. coli-Shigella clade, intact genes and gene fragments have been disseminated non-uniformly and at appreciable frequency, constructing communities that transgress environmental and lifestyle boundaries.

Show MeSH
Related in: MedlinePlus