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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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Connectivity and edge label value distribution of the directed obligate LGT network by E. coli phylogenetic groups.
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RSOB120112F8: Connectivity and edge label value distribution of the directed obligate LGT network by E. coli phylogenetic groups.

Mentions: Edges with label values greater than or equal to 5 are listed in table 2. The donor–recipient pairs with greatest total edge label are E. coli strains E24377A and IAI1, E. coli strains ED1a and CFT073, and E. coli strains E24377A and SE11. Each of these connections crosses recognized phylogenetic groups, and links a commensal with a pathogenic strain: barriers to transfer across groups and lifestyles can be low. On the other hand, 11 of 16 edges with label greater than or equal to 6 (69%) reflect intra-group transfer, consistent with the ready integration of incoming DNA via homologous recombination. Differing edge weight and connectivity distributions were observed across the E. coli phylogenetic groups and Shigella (figure 8). We next investigate the number and diversity of exchange partners, and frequencies of transfer, within and between phylogenetic groups.Table 2.


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

Skippington E, Ragan MA - Open Biol (2012)

Connectivity and edge label value distribution of the directed obligate LGT network by E. coli phylogenetic groups.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120112F8: Connectivity and edge label value distribution of the directed obligate LGT network by E. coli phylogenetic groups.
Mentions: Edges with label values greater than or equal to 5 are listed in table 2. The donor–recipient pairs with greatest total edge label are E. coli strains E24377A and IAI1, E. coli strains ED1a and CFT073, and E. coli strains E24377A and SE11. Each of these connections crosses recognized phylogenetic groups, and links a commensal with a pathogenic strain: barriers to transfer across groups and lifestyles can be low. On the other hand, 11 of 16 edges with label greater than or equal to 6 (69%) reflect intra-group transfer, consistent with the ready integration of incoming DNA via homologous recombination. Differing edge weight and connectivity distributions were observed across the E. coli phylogenetic groups and Shigella (figure 8). We next investigate the number and diversity of exchange partners, and frequencies of transfer, within and between phylogenetic groups.Table 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