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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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Related in: MedlinePlus

Properties of the directed obligate LGT network. Distribution of (a) connectivity and (b) edge labels. Filled bars denote out-degree; unfilled bars, in-degree.
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RSOB120112F2: Properties of the directed obligate LGT network. Distribution of (a) connectivity and (b) edge labels. Filled bars denote out-degree; unfilled bars, in-degree.

Mentions: We have recommended that a GEC be defined as a set of entities, each of which has over time both donated genetic material to, and received genetic material from, every other entity in that GEC, via a path of lateral transfer [5]. Does our E. coli–Shigella DOLN (figure 2) meet this stringent criterion? Recall that edges cannot be realized between sister termini, and that genetic material cannot flow backwards in time. Of 2072 potential edges, we observe only 462 (22.3%); however, 2072 (78.1%) of the 2704 possible node pairs are connected by a path of length greater than or equal to 1; that is, our E. coli–Shigella DOLN is densely connected, but, by our proposed criterion (above), falls short of qualifying as a GEC. Of the missing edges, many would connect closely related genomes (E. coli K-12 W3110 with K-12 MG1655; E. coli EDL933 with O157 : H7; strains within S. flexneri) among which LGT can often not be inferred owing to high sequence similarity. Including all possible (not only obligate) edits greatly increases the density of connection: 1925 (93%) of 2072 possible node pairs are connected by a path of length 1, and all possible node pairs (2072/2072, 100%) by a path of length greater than or equal to 1. Our inference may have missed other paths owing to incomplete or uneven sampling of genomes. Although the inferred connectivity of the DOLN falls short of our proposed criterion, we suspect, for the above reasons, that the E. coli–Shigella clade is in fact a GEC. This will be testable as more genomes in this clade are sequenced.Figure 2.


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

Skippington E, Ragan MA - Open Biol (2012)

Properties of the directed obligate LGT network. Distribution of (a) connectivity and (b) edge labels. Filled bars denote out-degree; unfilled bars, in-degree.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120112F2: Properties of the directed obligate LGT network. Distribution of (a) connectivity and (b) edge labels. Filled bars denote out-degree; unfilled bars, in-degree.
Mentions: We have recommended that a GEC be defined as a set of entities, each of which has over time both donated genetic material to, and received genetic material from, every other entity in that GEC, via a path of lateral transfer [5]. Does our E. coli–Shigella DOLN (figure 2) meet this stringent criterion? Recall that edges cannot be realized between sister termini, and that genetic material cannot flow backwards in time. Of 2072 potential edges, we observe only 462 (22.3%); however, 2072 (78.1%) of the 2704 possible node pairs are connected by a path of length greater than or equal to 1; that is, our E. coli–Shigella DOLN is densely connected, but, by our proposed criterion (above), falls short of qualifying as a GEC. Of the missing edges, many would connect closely related genomes (E. coli K-12 W3110 with K-12 MG1655; E. coli EDL933 with O157 : H7; strains within S. flexneri) among which LGT can often not be inferred owing to high sequence similarity. Including all possible (not only obligate) edits greatly increases the density of connection: 1925 (93%) of 2072 possible node pairs are connected by a path of length 1, and all possible node pairs (2072/2072, 100%) by a path of length greater than or equal to 1. Our inference may have missed other paths owing to incomplete or uneven sampling of genomes. Although the inferred connectivity of the DOLN falls short of our proposed criterion, we suspect, for the above reasons, that the E. coli–Shigella clade is in fact a GEC. This will be testable as more genomes in this clade are sequenced.Figure 2.

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