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Small variable segments constitute a major type of diversity of bacterial genomes at the species level

Fabrice Touzain1, Erick Denamur2, Claudine Médigue3, Valérie Barbe4, Meriem El Karoui1 and Marie-Agnès Petit1*

Author Affiliations

1 INRA, UMR1319, Micalis, Bat 222, Jouy en Josas, 78350, France

2 INSERM U722 and Université Paris 7, Faculté de Médecine, Site Xavier Bichat, Paris, 75018, France

3 CNRS-UMR 8030 & CEA/IG/Genoscope, Laboratoire d'Analyses Bioinformatiques en Génomique et Métabolisme (LABGeM), rue Gaston Crémieux, Evry, 91057, France

4 CEA, Institut de Génomique, Genoscope, rue Gaston Crémieux, Evry, 91057, France

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Genome Biology 2010, 11:R45  doi:10.1186/gb-2010-11-4-r45

Published: 30 April 2010

Additional files

Additional file 1:

Neighbor joining trees based on genomic MUMi distances of the strains selected for the maximal genomes alignments.

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Additional file 2:

Choice of the maximum divergence level for inclusion of ClustalW aligned sequences into the backbone.

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Additional file 3:

Distribution of the VS sizes in the five-genome alignments.

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Additional file 4:

List of genes containing microdiversity loci in the E. coli five-genome alignments.

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Additional file 5:

List of genes containing microdiversity loci in the E. coli B2 five-genome alignments.

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Open Data

Additional file 6:

List of genes containing microdiversity loci in the S. aureus five-genome alignments.

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Additional file 7:

List of genes containing microdiversity loci in the S. pyogenes five-genome alignments.

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Additional file 8:

Distribution of the E. coli genes containing microdiversity loci in functional categories.

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Open Data

Additional file 9:

List of genes placed downstream of microdiversity loci in the E. coli five-genome alignments.

Format: XLS Size: 51KB Download file

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Open Data

Additional file 10:

List of genes placed downstream of microdiversity loci in the E. coli B2 five-genome alignments.

Format: XLS Size: 33KB Download file

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Open Data

Additional file 11:

List of genes placed downstream of microdiversity loci in the S. aureus five-genome alignments.

Format: XLS Size: 71KB Download file

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Open Data

Additional file 12:

List of genes placed downstream of microdiversity loci in the S. pyogenes five-genome alignments.

Format: XLS Size: 35KB Download file

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Open Data

Additional file 13:

Distribution of the E. coli genes placed downstream of microdiversity loci in functional categories.

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Open Data

Additional file 14:

Loci occupancy in the five-genome alignments.

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