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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

Degree and betweenness of nodes (genomes) of the directed obligate LGT network (DOLN) as a function of the lengths of the corresponding shortest and longest root-to-leaf paths in the MRP tree. Because we inferred LGT by reference to a (temporal) phylogenetic tree, a node in the DOLN may represent an extant genome, or one inferred as ancestral in the MRP tree. Because there exists a path from every leaf in the MRP tree to the root, ancestral genomes fall on one or more of these paths. Scatterplots show weak to moderate downward trends. Black lines are best-fit first-order polynomials; rho (ρ) is the Spearman rank correlation coefficient.
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RSOB120112F5: Degree and betweenness of nodes (genomes) of the directed obligate LGT network (DOLN) as a function of the lengths of the corresponding shortest and longest root-to-leaf paths in the MRP tree. Because we inferred LGT by reference to a (temporal) phylogenetic tree, a node in the DOLN may represent an extant genome, or one inferred as ancestral in the MRP tree. Because there exists a path from every leaf in the MRP tree to the root, ancestral genomes fall on one or more of these paths. Scatterplots show weak to moderate downward trends. Black lines are best-fit first-order polynomials; rho (ρ) is the Spearman rank correlation coefficient.

Mentions: Among these extant genomes, environmental strain E. coli SMS-3–5 has donated genetic material to the largest number of other genomes, while the extra-intestinal pathogen E. coli IAI39 has accepted genetic material from the largest number (figure 4). As relatively few nodes separate each of these from the root of the MRP reference tree, it could be that their apparently heightened involvement in LGT is an artefact of sampling bias. To assess this possibility, for each genome in the MRP tree, we plotted the length of the shortest and of the longest root-to-leaf path on which it falls (as surrogates for sampling density in that portion of the MRP tree) against measures of connectedness (figure 5). Each plot shows a weak to moderate downward trend in the data. Specifically, Spearman's rank correlation coefficients for the comparison between path length and each of the connectivity measures range from −0.38 (betweenness versus maximum path length) to −0.11 (in-degree versus minimum path length). Thus, we find little evidence to suggest that relative phyletic coverage has affected our recovery of edit paths.Figure 4.


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

Skippington E, Ragan MA - Open Biol (2012)

Degree and betweenness of nodes (genomes) of the directed obligate LGT network (DOLN) as a function of the lengths of the corresponding shortest and longest root-to-leaf paths in the MRP tree. Because we inferred LGT by reference to a (temporal) phylogenetic tree, a node in the DOLN may represent an extant genome, or one inferred as ancestral in the MRP tree. Because there exists a path from every leaf in the MRP tree to the root, ancestral genomes fall on one or more of these paths. Scatterplots show weak to moderate downward trends. Black lines are best-fit first-order polynomials; rho (ρ) is the Spearman rank correlation coefficient.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120112F5: Degree and betweenness of nodes (genomes) of the directed obligate LGT network (DOLN) as a function of the lengths of the corresponding shortest and longest root-to-leaf paths in the MRP tree. Because we inferred LGT by reference to a (temporal) phylogenetic tree, a node in the DOLN may represent an extant genome, or one inferred as ancestral in the MRP tree. Because there exists a path from every leaf in the MRP tree to the root, ancestral genomes fall on one or more of these paths. Scatterplots show weak to moderate downward trends. Black lines are best-fit first-order polynomials; rho (ρ) is the Spearman rank correlation coefficient.
Mentions: Among these extant genomes, environmental strain E. coli SMS-3–5 has donated genetic material to the largest number of other genomes, while the extra-intestinal pathogen E. coli IAI39 has accepted genetic material from the largest number (figure 4). As relatively few nodes separate each of these from the root of the MRP reference tree, it could be that their apparently heightened involvement in LGT is an artefact of sampling bias. To assess this possibility, for each genome in the MRP tree, we plotted the length of the shortest and of the longest root-to-leaf path on which it falls (as surrogates for sampling density in that portion of the MRP tree) against measures of connectedness (figure 5). Each plot shows a weak to moderate downward trend in the data. Specifically, Spearman's rank correlation coefficients for the comparison between path length and each of the connectivity measures range from −0.38 (betweenness versus maximum path length) to −0.11 (in-degree versus minimum path length). Thus, we find little evidence to suggest that relative phyletic coverage has affected our recovery of edit paths.Figure 4.

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