L. A. Weinert, J. H. Werren, A. Aebi, G. N. Stone, and F. M. Jiggins, Evolution and diversity of Rickettsia bacteria, BMC Biol, vol.7, p.6, 2009.

V. Merhej and D. Raoult, Rickettsial evolution in the light of comparative genomics, Biol Rev Camb Philos Soc, vol.86, p.20716256, 2011.

P. Parola, C. D. Paddock, C. Socolovschi, M. B. Labruna, O. Mediannikov et al., Update on tickborne rickettsioses around the world: a geographic approach, Clin Microbiol Rev, vol.26, pp.657-702, 2013.

D. R. Stothard, J. B. Clark, and P. A. Fuerst, Ancestral divergence of Rickettsia bellii from the spotted fever and typhus groups of Rickettsia and antiquity of the genus Rickettsia, Int J Syst Bacteriol, vol.44, p.7981106, 1994.

D. Raoult and V. Roux, Rickettsioses as paradigms of new or emerging infectious diseases, Clin Microbiol Rev, vol.10, p.9336669, 1997.

J. O. Andersson and S. Andersson, Genome degradation is an ongoing process in Rickettsia, Mol Biol Evol, vol.16, p.10486973, 1999.

S. Andersson, A. Zomorodipour, J. O. Andersson, T. Sicheritz-ponten, U. Alsmark et al., The genome sequence of Rickettsia prowazekii and the origin of mitochondria, Nature, vol.396, p.9823893, 1998.

A. C. Darby, N. H. Cho, H. H. Fuxelius, J. Westberg, and S. G. Andersson, Intracellular pathogens go extreme: genome evolution in the Rickettsiales, Trends Genet, vol.23, p.17822801, 2007.

P. E. Fournier, E. Karkouri, K. Leroy, Q. Robert, C. Giumelli et al., Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction, BMC Genomics, vol.10, p.166, 2009.

S. K. Sahni, H. P. Narra, A. Sahni, and D. H. Walker, Recent molecular insights into rickettsial pathogenesis and immunity, Future Microbiol, vol.8, pp.1265-1288, 2013.

Y. Bechah, E. Karkouri, K. Mediannikov, O. Leroy, Q. Pelletier et al., Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities, Genome Res, vol.20, p.20368341, 2010.

M. P. Mcleod, X. Qin, S. E. Karpathy, J. Gioia, S. K. Highlander et al., Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae, J Bacteriol, vol.186, pp.5842-5855, 2004.

H. Ogata, S. Audic, P. Renesto-audiffren, P. E. Fournier, V. Barbe et al., Mechanisms of evolution in Rickettsia conorii and R. prowazekii, Science, vol.293, p.11557893, 2001.

H. Ogata, S. B. La, S. Audic, P. Renesto, G. Blanc et al., Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens, PLoS Genet, vol.2, 2006.

H. Ogata, P. Renesto, S. Audic, C. Robert, G. Blanc et al., The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite, PLoS Biol, vol.3, 2005.

G. Blanc, H. Ogata, C. Robert, S. Audic, J. M. Claverie et al., Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome, Genome Res, vol.17, p.17916642, 2007.

G. Blanc, H. Ogata, C. Robert, S. Audic, K. Suhre et al., Reductive genome evolution from the mother of Rickettsia, PLoS.Genet, vol.3, p.17238289, 2007.

D. W. Ellison, T. R. Clark, D. E. Sturdevant, K. Virtaneva, S. F. Porcella et al., Genomic comparison of virulent Rickettsia rickettsii Sheila Smith and avirulent Rickettsia rickettsii Iowa, Infect Immun, vol.76, p.18025092, 2008.

P. E. Fournier and D. Raoult, Intraspecies diversity of Rickettsia conorii, J Infect Dis, vol.199, pp.1097-1098, 2009.

R. F. Felsheim, T. J. Kurtti, and U. G. Munderloh, Genome sequence of the endosymbiont Rickettsia peacockii and comparison with virulent Rickettsia rickettsii: identification of virulence factors, PLoS ONE, vol.4, p.8361, 2009.

G. D. Baldridge, N. Y. Burkhardt, R. F. Felsheim, T. J. Kurtti, and U. G. Munderloh, Plasmids of the pRM/pRF family occur in diverse Rickettsia species, Appl Environ Microbiol, vol.74, p.18065613, 2008.

G. D. Baldridge, N. Y. Burkhardt, M. B. Labruna, R. C. Pacheco, C. D. Paddock et al., Wide dispersal and possible multiple origins of low-copy-number plasmids in rickettsia species associated with blood-feeding arthropods, Appl Environ Microbiol, vol.76, pp.1718-1731, 2010.

J. J. Gillespie, M. S. Beier, M. S. Rahman, N. C. Ammerman, J. M. Shallom et al., Plasmids and rickettsial evolution: insight from Rickettsia felis, PLoS ONE, vol.2, 2007.

S. Halary, J. W. Leigh, B. Cheaib, P. Lopez, and E. Bapteste, Network analyses structure genetic diversity in independent genetic worlds, Proc Natl Acad Sci U S A, vol.107, pp.127-132, 2010.

M. Tamminen, M. Virta, R. Fani, and M. Fondi, Large-scale analysis of plasmid relationships through genesharing networks, Mol Biol Evol, vol.29, pp.1225-1240, 2012.

S. Bocs, S. Cruveiller, D. Vallenet, G. Nuel, and C. Medigue, AMIGene: Annotation of MIcrobial Genes, Nucleic Acids Res, vol.31, p.12824403, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00271511

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSIBLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, p.9254694, 1997.

R. L. Tatusov, E. V. Koonin, and D. J. Lipman, A genomic perspective on protein families, Science, vol.278, pp.631-637, 1997.

D. M. Kristensen, L. Kannan, M. K. Coleman, Y. I. Wolf, A. Sorokin et al., A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches, Bioinformatics, vol.26, pp.1481-1487, 2010.

M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. Mcgettigan et al., Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, p.17846036, 2007.
DOI : 10.1093/bioinformatics/btm404
URL : https://hal.archives-ouvertes.fr/hal-00206210

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, p.15034147, 2004.
DOI : 10.1093/nar/gkh340
URL : https://academic.oup.com/nar/article-pdf/32/5/1792/7055030/gkh340.pdf

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis version 6.0, Mol Biol Evol, vol.30, pp.2725-2729, 2013.
DOI : 10.1093/molbev/mst197
URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf

C. Whidden, N. Zeh, and R. G. Beiko, Supertrees Based on the Subtree Prune-and-Regraft Distance, Syst Biol, vol.63, pp.566-581, 2014.
DOI : 10.7287/peerj.preprints.18v1
URL : https://peerj.com/preprints/18v1.pdf

P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang et al., Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, vol.13, p.14597658, 2003.

L. Guy, J. R. Kultima, and S. G. Andersson, genoPlotR: comparative gene and genome visualization in R, Bioinformatics, vol.26, pp.2334-2335, 2010.
DOI : 10.1093/bioinformatics/btq413
URL : https://academic.oup.com/bioinformatics/article-pdf/26/18/2334/546156/btq413.pdf

P. E. Fournier, L. Belghazi, C. Robert, E. Karkouri, K. Richards et al., Variations of Plasmid Content in Rickettsia felis, PLoS ONE, vol.3, p.18509454, 2008.
DOI : 10.1371/journal.pone.0002289
URL : https://doi.org/10.1371/journal.pone.0002289

K. Chan, S. Casjens, and N. Parveen, Detection of established virulence genes and plasmids to differentiate Borrelia burgdorferi strains, Infect Immun, vol.80, pp.1519-1529, 2012.
DOI : 10.1128/iai.06326-11
URL : http://iai.asm.org/content/80/4/1519.full.pdf

C. Smillie, M. P. Garcillan-barcia, M. V. Francia, E. P. Rocha, and F. De-la-cruz, Mobility of plasmids. Microbiol Mol Biol Rev, vol.74, p.20805406, 2010.

Y. I. Wolf and E. V. Koonin, Genome reduction as the dominant mode of evolution, Bioessays, vol.35, pp.829-837, 2013.

J. Zheng, D. Peng, L. Ruan, and M. Sun, Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group, BMC Evol Biol, vol.13, p.262, 2013.

Y. Feng, J. Liu, Y. G. Li, F. L. Cao, R. N. Johnston et al., Inheritance of the Salmonella virulence plasmids: mostly vertical and rarely horizontal, Infect Genet Evol, vol.12, pp.1058-1063, 2012.

J. A. Chapman, E. F. Kirkness, O. Simakov, S. E. Hampson, T. Mitros et al., The dynamic genome of Hydra, Nature, vol.464, pp.592-596, 2010.

T. Driscoll, J. J. Gillespie, E. K. Nordberg, A. F. Azad, and B. W. Sobral, Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont, Genome Biol Evol, vol.5, pp.621-645, 2013.

O. Duron, Lateral transfers of insertion sequences between Wolbachia, Cardinium and Rickettsia bacterial endosymbionts, Heredity, vol.111, pp.330-337, 2013.

Y. Yin and D. Fischer, On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer, BMC Evol Biol, vol.6, p.16914045, 2006.

I. Yomtovian, N. Teerakulkittipong, B. Lee, J. Moult, and R. Unger, Composition bias and the origin of ORFan genes, Bioinformatics, vol.26, pp.996-999, 2010.

D. Tautz and T. Domazet-loso, The evolutionary origin of orphan genes, Nat Rev Genet, vol.12, 2011.

P. Puigbò, A. E. Lobkovsky, D. M. Kristensen, Y. I. Wolf, and E. V. Koonin, Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes, BMC Biol, vol.21, 2014.

B. Snel and P. Bork, Genomes in flux: the evolution of archaeal and proteobacterial gene content, Genome Res, vol.12, p.11779827, 2002.

M. P. Garcillan-barcia, M. V. Francia, and F. De-la-cruz, The diversity of conjugative relaxases and its application in plasmid classification, FEMS Microbiol Rev, vol.33, p.19396961, 2009.

T. G. Torres, M. Pistorio, M. J. Althabegoiti, L. Cervantes, D. Wibberg et al., Rhizobial plasmid pLPU83a is able to switch between different transfer machineries depending on its genomic background, FEMS Microbiol Ecol, vol.88, p.24646299, 2014.

T. Kloesges, T. O. Popa, W. Martin, and T. Dagan, Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths, Mol Biol Evol, vol.28, pp.1057-1074, 2011.

M. S. Rahman, J. J. Gillespie, S. J. Kaur, K. T. Sears, S. M. Ceraul et al., Rickettsia typhi Possesses Phospholipase A(2) Enzymes that Are Involved in Infection of Host Cells, Plos Pathog, vol.9, p.1003399, 2013.

T. J. Johnson and L. K. Nolan, Pathogenomics of the virulence plasmids of Escherichia coli, Microbiol Mol Biol Rev, vol.73, pp.750-774, 2009.

N. Y. Burkhardt, G. D. Baldridge, P. C. Williamson, P. M. Billingsley, C. C. Heu et al., Development of shuttle vectors for transformation of diverse Rickettsia species, PloS ONE, vol.6, p.22216299, 2011.

D. O. Wood, A. Hines, A. M. Tucker, A. Woodard, L. O. Driskell et al., Establishment of a replicating plasmid in Rickettsia prowazekii, PloS ONE, vol.7, p.22529927, 2012.