Open Access Research article

Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome

Marco Fondi1, Giovanni Bacci1, Matteo Brilli2, Maria Cristiana Papaleo1, Alessio Mengoni1, Mario Vaneechoutte3, Lenie Dijkshoorn4 and Renato Fani1*

Author Affiliations

1 Laboratory of Microbial and Molecular Evolution, Dept. of Evolutionary Biology, Via Romana 17-19, University of Florence, I-50125 Florence, Italy

2 Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, Lyon, France

3 Laboratory Bacteriology Research, Faculty Medicine & Health Sciences, University of Ghent, Belgium

4 Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands

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BMC Evolutionary Biology 2010, 10:59  doi:10.1186/1471-2148-10-59

Published: 24 February 2010

Additional files

Additional file 1:

Identity relationships among all the proteins of the Acinetobacter plasmid dataset. All the proteins belonging to the same plasmid (nodes) are circularly arranged and are linked to the others according to the identity value they share. Three different identity thresholds are shown (60%, 70%, 80%). Plasmids names have been colored according to the habitat of their source microorganism: yellow indicates clinical sources, green indicates environmental sources, grey indicates that habitat information was not available.

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Additional file 2:

The organization of the mer operon in pKLH plasmids. Schematic representation of the organization of the mer operon within the pKLH plasmid family.

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Additional file 3:

Functional assignment analysis of the plasmid proteins that remained isolated during network construction. a) COG functional assignment of the 280 proteins that remained isolated in the construction of the plasmid networks (see text for details of networks construction). In b), c) and d) the details of "cellular processes", "metabolism" and "information" categories are reported, respectively.

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Additional file 4:

Phylogenetic profiling and identification codes at 100% and 50% identity thresholds. Neighbor joining dendrograms built using the Jaccard distance matrix values (see text for details) obtained with a threshold of 100% for plasmids (a) and protein clusters (b). Neighbor joining dendrograms of protein clusters with representative GI codes. at 50% (c) and 100% (d) identity thresholds.

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Additional file 5:

Similarity, identity based, networks of plasmid and chromosome proteins. Similarity relationships between the proteins of the Acinetobacter plasmid dataset and mini-chromosome proteins (see text for mini-chromosomes dataset construction) at 60%, 70%, 80% identity thresholds. Mini-chromosomes are shown in the center and plasmids are circularly arranged. Identity thresholds are shown on the bottom right of the figure. Abbreviations: Ac. b., Acinetobacter baumannii

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