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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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Distribution of betweenness centrality for nodes of the directed obligate LGT network (DOLN).
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RSOB120112F6: Distribution of betweenness centrality for nodes of the directed obligate LGT network (DOLN).

Mentions: Betweenness is a measure of node centrality defined [46] as the frequency at which a given node lies on the shortest path between any pair of nodes in a network. High-betweenness nodes are important because they intermediate between genomes, other genetic entities and/or communities that do not exchange genes directly. Figure 6 shows the distribution of betweenness centrality for nodes of our E. coli–Shigella DOLN. The three genomes with highest node betweenness are the environmental strain E. coli SMS-3–5, and the extra-intestinal pathogens E. coli IAI39 and UMN026. Although this measure shows a moderate degree of potential sampling bias (figure 5), high-betweenness nodes clearly are present in our DOLN. We next investigate their potential role in constructing the E. coli–Shigella GEC, focusing on frequencies and pathways of transfer within and between phyletic groups, lifestyles and habitats.Figure 6.


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

Skippington E, Ragan MA - Open Biol (2012)

Distribution of betweenness centrality for nodes of the directed obligate LGT network (DOLN).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120112F6: Distribution of betweenness centrality for nodes of the directed obligate LGT network (DOLN).
Mentions: Betweenness is a measure of node centrality defined [46] as the frequency at which a given node lies on the shortest path between any pair of nodes in a network. High-betweenness nodes are important because they intermediate between genomes, other genetic entities and/or communities that do not exchange genes directly. Figure 6 shows the distribution of betweenness centrality for nodes of our E. coli–Shigella DOLN. The three genomes with highest node betweenness are the environmental strain E. coli SMS-3–5, and the extra-intestinal pathogens E. coli IAI39 and UMN026. Although this measure shows a moderate degree of potential sampling bias (figure 5), high-betweenness nodes clearly are present in our DOLN. We next investigate their potential role in constructing the E. coli–Shigella GEC, focusing on frequencies and pathways of transfer within and between phyletic groups, lifestyles and habitats.Figure 6.

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