Lateral genomics, Trends in Cell Biology, vol.9, issue.12, pp.5-8, 1999. ,
DOI : 10.1016/S0962-8924(99)01664-5
Horizontal Gene Transfer in Prokaryotes: Quantification and Classification, Annual Review of Microbiology, vol.55, issue.1, pp.709-742, 2001. ,
DOI : 10.1146/annurev.micro.55.1.709
Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, issue.6784, pp.299-304, 2000. ,
DOI : 10.1038/35012500
Horizontal Gene Transfer Accelerates Genome Innovation and Evolution, Molecular Biology and Evolution, vol.20, issue.10, pp.1598-1602, 2003. ,
DOI : 10.1093/molbev/msg154
URL : http://mbe.oxfordjournals.org/cgi/content/short/20/10/1598
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria, Biology Direct, vol.4, issue.1, p.13, 2009. ,
DOI : 10.1186/1745-6150-4-13
URL : https://hal.archives-ouvertes.fr/hal-00831226
Computational inference of scenarios for ??-proteobacterial genome evolution, Proceedings of the National Academy of Sciences, vol.101, issue.26, pp.9722-9727, 2004. ,
DOI : 10.1073/pnas.0400975101
URL : https://hal.archives-ouvertes.fr/hal-00427550
Tsutsugamushi disease in World War II, J Parasitology, vol.34, issue.3, pp.169-191, 1948. ,
Orientia tsutsugamushi infection: overview and immune responses. Microbes and Infection, Institut Pasteur, vol.3, pp.11-21, 2001. ,
DOI : 10.1016/s1286-4579(00)01352-6
Classification of Rickettsia tsutsugamushi in a New Genus, Orientia gen. nov., as Orientia tsutsugamushi comb. nov., International Journal of Systematic Bacteriology, vol.45, issue.3, pp.45589-591, 1995. ,
DOI : 10.1099/00207713-45-3-589
Rickettsioses in Africa: A paradigm of new or emerging infectious diseases, International Journal of Infectious Diseases, vol.21, issue.4, pp.694-719, 1997. ,
DOI : 10.1016/j.ijid.2014.03.561
Rickettsial evolution in the light of comparative genomics, Biological Reviews, vol.452, issue.4, pp.379-405, 2011. ,
DOI : 10.1111/j.1469-185X.2010.00151.x
Wolbachia: evolutionary novelty in a rickettsial bacteria, BMC Evolutionary Biology, vol.1, issue.1, p.10, 2001. ,
DOI : 10.1186/1471-2148-1-10
Identification of a granulocytotropic Ehrlichia species as the etiologic agent of human disease, J Clin Microbiol, vol.32, issue.3, pp.589-595, 1994. ,
Ehrlichia chaffeensis, a new species associated with human ehrlichiosis, J Clin Microbiol, vol.29, issue.12, pp.2838-2842, 1991. ,
Isolation and characterization of an Ehrlichia sp. from a patient diagnosed with human ehrlichiosis, J Clin Microbiol, issue.12, pp.292741-2745, 1991. ,
Wolbachia genome integrated in an insect chromosome: Evolution and fate of laterally transferred endosymbiont genes, Genome Research, vol.18, issue.2, pp.272-280, 2008. ,
DOI : 10.1101/gr.7144908
A Robust Species Tree for the Alphaproteobacteria, Journal of Bacteriology, vol.189, issue.13, pp.4578-4586, 2007. ,
DOI : 10.1128/JB.00269-07
Phylogenomic Analysis of Odyssella thessalonicensis Fortifies the Common Origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana Mitochondrion, PLoS ONE, vol.293, issue.9, p.24857, 2011. ,
DOI : 10.1371/journal.pone.0024857.s001
Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci rep, p.13, 2011. ,
Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade, Molecular Biology and Evolution, vol.29, issue.2, pp.599-615, 2011. ,
DOI : 10.1093/molbev/msr203
A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade, PLoS ONE, vol.23, issue.9, p.24457, 2011. ,
DOI : 10.1371/journal.pone.0024457.s010
The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria, PLoS ONE, vol.56, issue.1, p.30520, 2012. ,
DOI : 10.1371/journal.pone.0030520.s017
Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths, Molecular Biology and Evolution, vol.28, issue.2, pp.1057-1074, 2011. ,
DOI : 10.1093/molbev/msq297
The Rhizome of Life: The Sympatric Rickettsia felis Paradigm Demonstrates the Random Transfer of DNA Sequences, Molecular Biology and Evolution, vol.28, issue.11, pp.283213-3223, 2011. ,
DOI : 10.1093/molbev/msr239
URL : https://hal.archives-ouvertes.fr/hal-01105200
Gene gain and loss events in Rickettsia and Orientia species, Biology Direct, vol.6, issue.1, p.6, 2011. ,
DOI : 10.1093/nar/gkh340
Genome Sequence of Rickettsia bellii Illuminates the Role of Amoebae in Gene Exchanges between Intracellular Pathogens, PLoS Genetics, vol.36, issue.5, p.76, 2006. ,
DOI : 10.1371/journal.pgen.0020076.st008
Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome, Genome Research, vol.17, issue.11, pp.1657-1664, 2007. ,
DOI : 10.1101/gr.6742107
The source of laterally transferred genes in bacterial genomes, Genome Biology, vol.4, issue.9, p.57, 2003. ,
DOI : 10.1186/gb-2003-4-9-r57
URL : https://hal.archives-ouvertes.fr/hal-00427389
Molecular archaeology of the Escherichia coli genome, Proceedings of the National Academy of Sciences, vol.95, issue.16, pp.9413-9417, 1998. ,
DOI : 10.1073/pnas.95.16.9413
Detection of Genes with Atypical Nucleotide Sequence in Microbial Genomes, Journal of Molecular Evolution, vol.54, issue.3, pp.365-375, 2002. ,
DOI : 10.1007/s00239-001-0051-8
Genomic signature is preserved in short DNA fragments, Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering, p.6, 2000. ,
DOI : 10.1109/BIBE.2000.889603
Detection and characterization of horizontal transfers in prokaryotes using genomic signature, Nucleic Acids Research, vol.33, issue.1, p.6, 2005. ,
DOI : 10.1093/nar/gni004
An Approximately Unbiased Test of Phylogenetic Tree Selection, Systematic Biology, vol.51, issue.3, pp.492-508, 2002. ,
DOI : 10.1080/10635150290069913
Visualization of the phylogenetic content of five genomes using dekapentagonal maps, Genome Biology, vol.5, issue.3, p.20, 2004. ,
DOI : 10.1186/gb-2004-5-3-r20
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events, Genome Research, vol.16, issue.9, pp.1099-1108, 2006. ,
DOI : 10.1101/gr.5322306
Genome phylogeny based on gene content, Nature Genetics, vol.21, issue.1, pp.108-110, 1999. ,
DOI : 10.1038/5052
Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content, Genome Research, vol.12, issue.1, pp.17-25, 2002. ,
DOI : 10.1101/gr.176501
Rapid evolutionary innovation during an Archaean genetic expansion, Nature, vol.15, issue.7328, pp.93-96 ,
DOI : 10.1038/nature09649
URL : http://hdl.handle.net/1721.1/61263
The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Research, vol.28, issue.1, pp.33-36, 2000. ,
DOI : 10.1093/nar/28.1.33
The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Research, vol.29, issue.1, pp.22-28, 2001. ,
DOI : 10.1093/nar/29.1.22
Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000. ,
DOI : 10.1038/75556
Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti, BMC Genomics, vol.10, issue.1, p.33, 2009. ,
DOI : 10.1186/1471-2164-10-33
Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements, PLoS Biology, vol.265, issue.3, p.69, 2004. ,
DOI : 10.1371/journal.pbio.0020069.st009
The Genealogic Tree of Mycobacteria Reveals a Long-Standing Sympatric Life into Free-Living Protozoa, PLoS ONE, vol.18, issue.4, p.34754 ,
DOI : 10.1371/journal.pone.0034754.s010
URL : https://hal.archives-ouvertes.fr/hal-00831103
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms, Proceedings of the National Academy of Sciences, vol.106, issue.51, pp.10621848-21853, 2009. ,
DOI : 10.1073/pnas.0911354106
Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution, FEMS Microbiology Reviews, vol.34, issue.3, pp.281-94, 2010. ,
DOI : 10.1111/j.1574-6976.2009.00209.x
Amoeba/Amoebal Symbiont Genetic Transfers: Lessons from Giant Virus Neighbours, Intervirology, vol.53, issue.5, pp.254-67 ,
DOI : 10.1159/000312910
Phagocytosis of Cryptococcus neoformans by, and Nonlytic Exocytosis from, Acanthamoeba castellanii, Applied and Environmental Microbiology, vol.76, issue.18, pp.766056-6062, 2010. ,
DOI : 10.1128/AEM.00812-10
Amoebae as Genitors and Reservoirs of Giant Viruses, Intervirology, vol.53, issue.5, pp.321-330 ,
DOI : 10.1159/000312917
Ticks, Journal of Medical Entomology, vol.41, issue.3, pp.277-286, 2004. ,
DOI : 10.1603/0022-2585-41.3.277
Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants, Mobile genet elem 2012, pp.81-87 ,
DOI : 10.1186/1471-2164-9-422
URL : https://hal.archives-ouvertes.fr/hal-00862309
Massive Horizontal Gene Transfer in Bdelloid Rotifers, Science, vol.320, issue.5880, pp.1210-1213, 2008. ,
DOI : 10.1126/science.1156407
Distribution and Evolution of Bacteriophage WO in Wolbachia, the Endosymbiont Causing Sexual Alterations in Arthropods, Journal of Molecular Evolution, vol.51, issue.5, pp.491-497, 2000. ,
DOI : 10.1007/s002390010112
Bacteriophage WO and Virus-like Particles in Wolbachia, an Endosymbiont of Arthropods, Biochemical and Biophysical Research Communications, vol.283, issue.5, pp.1099-1104, 2001. ,
DOI : 10.1006/bbrc.2001.4906
Mobile genetic elements: the agents of open source evolution, Nature Reviews Microbiology, vol.11, issue.9, pp.722-754, 2005. ,
DOI : 10.1093/nar/gkh059
Shewanella spp. Genomic Evolution for a Cold Marine Lifestyle and In-Situ Explosive Biodegradation, PLoS ONE, vol.5, issue.2, p.9109, 2010. ,
DOI : 10.1371/journal.pone.0009109.s002
The genomic code: inferring Vibrionaceae niche specialization, Nature Reviews Microbiology, vol.65, issue.9, pp.697-704, 2006. ,
DOI : 10.1038/nrmicro1476
Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea, The ISME Journal, vol.148, issue.1, pp.131-140, 2011. ,
DOI : 10.3354/ame013063
High Frequency of Horizontal Gene Transfer in the Oceans, Science, vol.330, issue.6000, p.33050, 2010. ,
DOI : 10.1126/science.1192243
The contribution of mobile genetic elements to the evolution and ecology of Vibrios, FEMS Microbiology Ecology, vol.74, issue.3, pp.485-499, 2010. ,
DOI : 10.1111/j.1574-6941.2010.00937.x
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends in Genet, pp.442-444, 1998. ,
The post-Darwinist rhizome of life, The Lancet, vol.375, issue.9709, pp.104-105, 2010. ,
DOI : 10.1016/S0140-6736(09)61958-9
A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes, Genome Biology, vol.10, issue.6, p.65, 2009. ,
DOI : 10.1186/gb-2009-10-6-r65
URL : https://hal.archives-ouvertes.fr/hal-00397761
Some lessons from Rickettsia genomics. FEMS, journal=Microbiol Rev, pp.99-117, 2005. ,
Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis, Science, vol.282, issue.5389, pp.282754-759, 1998. ,
DOI : 10.1126/science.282.5389.754
Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. Trends in Genet: TIG, pp.173-175, 1999. ,
The genome sequence of Rickettsia prowazekii and the origin of mitochondria, Nature, issue.6707, pp.396133-140, 1998. ,
History of the ADP/ATP-Translocase-Encoding Gene, a Parasitism Gene Transferred from a Chlamydiales Ancestor to Plants 1 Billion Years Ago, Applied and Environmental Microbiology, vol.69, issue.9, pp.5530-5535, 2003. ,
DOI : 10.1128/AEM.69.9.5530-5535.2003
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003. ,
DOI : 10.1101/gr.1224503
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.253389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
Graph clustering by flow simulation The Netherlands, 2000. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
DOI : 10.1093/nar/gkh340
URL : http://doi.org/10.1093/nar/gkh340
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.282731-282740, 2011. ,
DOI : 10.1093/molbev/msr121
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203626
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees, BMC Bioinformatics, vol.10, issue.1, pp.2981471-2148243, 2009. ,
DOI : 10.1186/1471-2105-10-298
URL : https://hal.archives-ouvertes.fr/inserm-00663932
Prolog: the language and its implementation compared with Lisp, Symposium on Artifical Intelligence and Programming Languages, pp.109-124 ,
Minimal Mutation Trees of Sequences, SIAM J App Methamatics, pp.35-42 ,
DOI : 10.1137/0128004
Origins of new genes and pseudogenes In Nature Education Available at, http://www.nature.com/scitable/ topicpage/origins-of-new-genes-and-pseudogenes-835, 2008. ,
FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform, BMC Bioinformatics, vol.6, issue.1, p.198, 2005. ,
DOI : 10.1186/1471-2105-6-198
Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX. Evolutionary bioinf online 2012, pp.417-421 ,
improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids res, pp.224673-4680, 1994. ,
Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998. ,
DOI : 10.1093/bioinformatics/14.9.755
Phylogenetic Analysis Using Parsimony (*and Other Method), 2003. ,
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002. ,
DOI : 10.1093/bioinformatics/18.3.502
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea, Journal of Molecular Evolution, vol.46, issue.2, pp.170-179, 1989. ,
DOI : 10.1007/BF02100115
Integration of Evolutionary Biology Concepts for Functional Annotation and Automation of Complex Research in Evolution: The Multi-Agent Software System DAGOBAH. In Evolutionary Biology - Concepts, Biodiversity, Marcroevolution and Genome Evolution, pp.71-76 ,
URL : https://hal.archives-ouvertes.fr/hal-00827323
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Bioinformatics, vol.25, issue.17, pp.252286-2288, 2009. ,
DOI : 10.1093/bioinformatics/btp368
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process, Molecular Biology and Evolution, vol.21, issue.6, pp.1095-1109, 2004. ,
DOI : 10.1093/molbev/msh112
URL : https://hal.archives-ouvertes.fr/lirmm-00108585
ACLAME: A CLAssification of Mobile genetic Elements, update 2010, Nucleic Acids Research, vol.38, issue.Database, pp.38-57, 2010. ,
DOI : 10.1093/nar/gkp938
GeneInfoViz: constructing and visualizing gene relation networks, In silico biol, vol.4, issue.3, pp.323-333, 2004. ,
The chordate proteome history database. Evolutionary bioinf online, pp.437-447, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00831115
An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales, BMC Evolutionary Biology, vol.12, issue.1, p.243, 2012. ,
DOI : 10.1093/molbev/msh112
URL : https://hal.archives-ouvertes.fr/inserm-00789846