Open Access Highly Accessed Research article

Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction

Pierre-Edouard Fournier1, Khalid El Karkouri1, Quentin Leroy1, Catherine Robert1, Bernadette Giumelli1, Patricia Renesto1, Cristina Socolovschi1, Philippe Parola1, Stéphane Audic2 and Didier Raoult1*

Author Affiliations

1 Unité des rickettsies, IFR 48 CNRS UMR 6020, Faculté de médecine, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France

2 Information Génomique et Structurale, CNRS UPR2589, Institut de Biologie structurale et Microbiologie, Marseille, France

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BMC Genomics 2009, 10:166  doi:10.1186/1471-2164-10-166

Published: 20 April 2009

Additional files

Additional file 1:

Gene content of the R. africae plasmid. GenBank accession number sare indicated in square brackets. The Table includes a comparison of rickettsial plasmid contents.

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Additional file 2:

R. africae gene content. The Table includes the gene content of the R. africae genome.

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Additional file 3:

Inversion observed by alignment of the R. africae (up) and R. conorii (down) genomes. The Figure shows an alignment of the R. conorii and R. africae genomes.

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Additional file 4:

Schematic representation of the genes diversely conserved in R. africae in comparison with highly pathogenic rickettsiae. The state of a gene is represented by a small box colored in green (full-length), blue (pseudogene), red (fragment), orange (remnant) or black (absent).Gene numbers are indicated in the left column. The Figure shows the gene distribution in R. africae by comparison with highly pathogenic rickettsiae.

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Additional file 5:

PCR-detection of R. africae and in Amblyomma ticks. Results are indicated as number of ticks positive/number tested. The Table includes the results from PCR detection of the R. africae chromosome and plasmid in ticks.

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Additional file 6:

Rickettsia africae strains used in this study. The table lists all R. africae strains used in this study.

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Additional file 7:

Phylogenetic tree showing the organization of spoT genes in Rickettsia species. Phylogenetic relationships were inferred from aligned sequences using the Mega3.1 software with the Neighbor-Joining method. Bootstrap values are indicated at the nodes. The Figure is a phylogenetic tree showing the organization of spoT genes in Rickettsia species.

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Additional file 8:

R. africae ORFs compared to other available Rickettsia genomes. The table details the distribution of R. africae ORF in other rickettsial genomes.

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Additional file 9:

Phylogenetic tree showing the organization of sca genes in Rickettsia species. Phylogenetic relationships were inferred from aligned sequences using the Mega3.1 software with the Neighbor-Joining method. Bootstrap values are indicated at the nodes. The Figure is a phylogenetic tree showing the organization of sca genes in Rickettsia species.

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Additional file 10:

Phylogenetic tree showing the organization of adr genes in Rickettsia species. Phylogenetic relationships were inferred from aligned sequences using the Mega3.1 software with the Neighbor-Joining method. Bootstrap values are indicated at the nodes. The Figure is a phylogenetic tree showing the organization of adr genes in Rickettsia species.

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Additional file 11:

Features of RickA repeat proline-rich motif in R. africae and other SFG rickettsiae. The motif " [EDGKQG]- [NS]-N- [IV]- [PSLTR](0,28)" was used to extract these repeats using a PatternMatchingtool. The table details RickA repeat proline-rich motifs in R. africae and other SFG rickettsiae.

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Additional file 12:

Phylogenetic tree showing the organization of virB6-2 genes in Rickettsia species. Phylogenetic relationships were inferred from aligned sequences using the Mega3.1 software with the Neighbor-Joining method. Bootstrap values are indicated at the nodes. The Figure is a phylogenetic tree showing the organization of virB6-2 genes in Rickettsia species.

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Additional file 13:

Comparison of epidemiological and clinical characteristics of Rickettsia species. The table includes data about the epidemiological and clinical characteristics of Rickettsia species.

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Additional file 14:

Immunohistochemical detection of R. africae (arrows) in the inoculation eschar of a patient with ATBF (monoclonal rabbit anti-R. africae antibody used at a dilution of 1:1,000 and hematoxylin counterstain; original magnification ×250). The Figure shows the presence of R. africae in the inoculation eschar of a patient with ATBF, revealed by immunohistochemistry.

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Additional file 15:

Supplementary material and methods. The data provided include detailed material and methods that were used for the genome sequencing and sequence analysis of R. africae.

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