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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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Plots comparing network properties ((a) shortest path length, (b) betweenness and (c) degree) of extant E. coli strains by lifestyle and habitat for the directed obligate LGT network (DOLN).
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RSOB120112F9: Plots comparing network properties ((a) shortest path length, (b) betweenness and (c) degree) of extant E. coli strains by lifestyle and habitat for the directed obligate LGT network (DOLN).

Mentions: We compared network properties (here, node degree and betweenness) of strains in these categories pairwise to determine whether they distinguish lateral relationships between groups. IPEC and ExPEC strains face distinct environments but share a pathogenic lifestyle. We find no evidence of significant difference between IPEC and ExPEC strains with regard to degree or betweenness (p = 0.70 and p = 0.48 respectively, by pairwise Wilcoxon rank sum test, Holm-adjusted; figure 9). We similarly compared the commensal strains versus each of these two pathogenic categories. In our DOLN, commensal and IPEC strains exhibit comparable degree (p = 1.00) and betweenness centrality (p = 0.61, both by pairwise Wilcoxon rank sum test, Holm-adjusted; figure 9). The commensal and ExPEC strains likewise exhibit comparable degree (p = 1.00) and betweenness centrality (p = 0.61, also by pairwise Wilcoxon rank sum test, Holm-adjusted; figure 9). Thus, these network properties fail to distinguish lateral relationships among these groups of commensal, IPEC and ExPEC strains.FigureĀ 9.


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

Skippington E, Ragan MA - Open Biol (2012)

Plots comparing network properties ((a) shortest path length, (b) betweenness and (c) degree) of extant E. coli strains by lifestyle and habitat for the directed obligate LGT network (DOLN).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120112F9: Plots comparing network properties ((a) shortest path length, (b) betweenness and (c) degree) of extant E. coli strains by lifestyle and habitat for the directed obligate LGT network (DOLN).
Mentions: We compared network properties (here, node degree and betweenness) of strains in these categories pairwise to determine whether they distinguish lateral relationships between groups. IPEC and ExPEC strains face distinct environments but share a pathogenic lifestyle. We find no evidence of significant difference between IPEC and ExPEC strains with regard to degree or betweenness (p = 0.70 and p = 0.48 respectively, by pairwise Wilcoxon rank sum test, Holm-adjusted; figure 9). We similarly compared the commensal strains versus each of these two pathogenic categories. In our DOLN, commensal and IPEC strains exhibit comparable degree (p = 1.00) and betweenness centrality (p = 0.61, both by pairwise Wilcoxon rank sum test, Holm-adjusted; figure 9). The commensal and ExPEC strains likewise exhibit comparable degree (p = 1.00) and betweenness centrality (p = 0.61, also by pairwise Wilcoxon rank sum test, Holm-adjusted; figure 9). Thus, these network properties fail to distinguish lateral relationships among these groups of commensal, IPEC and ExPEC strains.FigureĀ 9.

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