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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 shortest paths for the directed obligate LGT network. Zero-length paths represent self-connections (e.g. genome A to itself).
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RSOB120112F3: Distribution of shortest paths for the directed obligate LGT network. Zero-length paths represent self-connections (e.g. genome A to itself).

Mentions: The shortest paths between genome pairs in our DOLN (figure 3) range from zero to four steps in length, with most (1610/2072, 77.7%) pairs connected by a path of length more than or equal to 2. Although somewhat inflated because LGT cannot be inferred between sister termini, this proportion nonetheless indicates a breadth of genetic connectivity across the clade, expanding the possibility for DNA to flow into groups or communities not accessible in a single step from the donor genome.FigureĀ 3.


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 shortest paths for the directed obligate LGT network. Zero-length paths represent self-connections (e.g. genome A to itself).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120112F3: Distribution of shortest paths for the directed obligate LGT network. Zero-length paths represent self-connections (e.g. genome A to itself).
Mentions: The shortest paths between genome pairs in our DOLN (figure 3) range from zero to four steps in length, with most (1610/2072, 77.7%) pairs connected by a path of length more than or equal to 2. Although somewhat inflated because LGT cannot be inferred between sister termini, this proportion nonetheless indicates a breadth of genetic connectivity across the clade, expanding the possibility for DNA to flow into groups or communities not accessible in a single step from the donor genome.FigureĀ 3.

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