Lateral gene transfer as a support for the tree of life, Proc Natl Acad Sci U S A, vol.109, issue.13, pp.4962-4967, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00752055
Gene ontology: tool for the unification of biology, Nat Genet, vol.25, issue.1, pp.25-29, 2000. ,
Multilocus sequence-based analysis delineates a clonal population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of human origin, J Bacteriol, vol.193, issue.10, pp.2608-2618, 2011. ,
Coordinated regulation of species-specific hydroxycinnamic acid degradation and siderophore biosynthesis pathways in Agrobacterium fabrum, Appl Environ Microbiol, vol.82, issue.12, pp.3515-3524, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01910930
TPMS: a set of utilities for querying collections of gene trees, BMC Bioinformatics, vol.14, p.109, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00972257
Analysis of hydroxycinnamic acid degradation in Agrobacterium fabrum reveals a coenzyme A-dependent, betaoxidative deacetylation pathway, Appl Environ Microbiol, vol.80, issue.11, pp.3341-3349, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02001304
The origins of ecological diversity in prokaryotes, Curr Biol, vol.18, issue.21, pp.1024-1034, 2008. ,
Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity, Microb Ecol, vol.60, issue.4, pp.862-872, 2010. ,
Ancestral reconstruction by asymmetric wagner parsimony over continuous characters and squared parsimony over distributions, pp.72-86, 2008. ,
Epidemic clones, oceanic gene pools, and eco-LD in the free living marine pathogen Vibrio parahaemolyticus, Mol Biol Evol, vol.32, issue.6, pp.1396-1410, 2015. ,
The source of laterally transferred genes in bacterial genomes, Genome Biol, vol.4, issue.9, p.57, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-00427389
Rapid evolutionary innovation during an Archaean genetic expansion, Nature, vol.469, issue.7328, pp.93-96, 2011. ,
Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti, Nat Commun, vol.7, p.12219, 2016. ,
The UniProt-GO annotation database in 2011, Nucleic Acids Res, vol.40, pp.565-570, 2012. ,
Horizontally transferred genes cluster spatially and metabolically, Biol Direct, vol.10, p.72, 2015. ,
Is junk DNA bunk? A critique of ENCODE, Proc Natl Acad Sci U S A, vol.110, issue.14, pp.5294-5300, 2013. ,
Models, algorithms and programs for phylogeny reconciliation, Brief Bioinform, vol.12, issue.5, pp.392-400, 2011. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00825041
Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae, PLoS Genet, vol.8, issue.8, p.1002868, 2012. ,
PHYLIP (Phylogeny Inference Package) version 3.5c, 1993. ,
Experimental studies on the struggle for existence. I. Mixed population of two species of yeast, J Exp Biol, vol.9, pp.389-402, 1932. ,
Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58, Science, vol.294, issue.5550, pp.2323-2328, 2001. ,
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst Biol, vol.52, issue.5, pp.696-704, 2003. ,
Genome sequence and mutational analysis of plantgrowth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286 isolated from a zinc-lead mine tailing, Appl Environ Microbiol, vol.78, issue.15, pp.5384-5394, 2012. ,
Genome sequence of the arsenite-oxidizing strain Agrobacterium tumefaciens 5A, J Bacteriol, vol.194, issue.4, p.903, 2012. ,
Introducing the bacterial 'chromid': not a chromosome, Trends Microbiol, vol.18, issue.4, pp.141-148, 2010. ,
Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in 8 species of gamma-proteobacteria, Mol Biol Evol, vol.24, issue.3, pp.805-813, 2007. ,
Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus, Science, vol.344, issue.6182, pp.416-420, 2014. ,
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus, PLoS Genet, vol.3, issue.12, p.231, 2007. ,
Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis, Appl Environ Microbiol, vol.80, issue.16, pp.4842-4853, 2014. ,
, Computational Methods for Gene Orthology Inference. Brief Bioinform, vol.12, issue.5, pp.379-391, 2011.
Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum, Open Biol, vol.5, issue.1, p.140133, 2015. ,
The consequences of genetic drift for bacterial genome complexity, Genome Res, vol.19, issue.8, pp.1450-1454, 2009. ,
Versatile and open software for comparing large genomes, Genome Biol, vol.5, issue.2, p.12, 2004. ,
Insights from 20 years of bacterial genome sequencing, Funct Integr Genomics, vol.15, issue.2, pp.141-161, 2015. ,
Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens, Genome Biol Evol, vol.3, pp.762-781, 2011. ,
URL : https://hal.archives-ouvertes.fr/halsde-00723400
Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis, Res Microbiol, vol.166, issue.10, pp.729-741, 2015. ,
Amelioration of bacterial genomes: rates of change and exchange, J Mol Evol, vol.44, issue.4, pp.383-397, 1997. ,
Selfish operons: horizontal transfer may drive the evolution of gene clusters, Genetics, vol.143, issue.4, pp.1843-1860, 1996. ,
Genome sequence of Agrobacterium tumefaciens strain F2, a bioflocculant-producing bacterium, J. Bacteriol, vol.193, pp.5531-5531, 2011. ,
Comparative genomics of the lactic acid bacteria, Proc Natl Acad Sci U S A, vol.103, issue.42, pp.15611-15616, 2006. ,
High-quality sequence clustering guided by network topology and multiple alignment likelihood, Bioinformatics, 2012. ,
DOI : 10.1093/bioinformatics/bts098
URL : https://hal.archives-ouvertes.fr/hal-00965711
Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations, Syst Appl Microbiol, vol.38, issue.2, pp.84-90, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01222893
Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics, Syst Appl Microbiol, vol.38, issue.4, pp.287-291, 2015. ,
Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol.10, issue.6, p.3, 2009. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00400099
Semantic similarity in biomedical ontologies, PLoS Comput Biol, vol.5, issue.7, p.1000443, 2009. ,
DOI : 10.1371/journal.pcbi.1000443
URL : https://doi.org/10.1371/journal.pcbi.1000443
Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers, Appl Environ Microbiol, vol.72, issue.11, pp.7123-7131, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00428025
Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the, 2014. ,
, Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid, Mol Phylogenet Evol, vol.73, pp.202-207
The organization of the bacterial genome, Annu Rev Genet, vol.42, pp.211-233, 2008. ,
Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche, Science, vol.348, pp.1019-1023, 2015. ,
Genome sequence of the curdlan-producing Agrobacterium sp. strain ATCC 31749, J Bacteriol, vol.193, issue.16, pp.4294-4295, 2011. ,
A new measure for functional similarity of gene products based on Gene Ontology, BMC Bioinformatics, vol.7, p.302, 2006. ,
Representing a set of reconciliations in a compact way, J Bioinform Comput Biol, vol.11, issue.2, p.1250025, 2012. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00818801
Progressive genome-wide introgression in agricultural Campylobacter coli, Mol Ecol, vol.22, issue.4, pp.1051-1064, 2013. ,
Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium, Appl Environ Microbiol, vol.79, issue.4, pp.1414-1417, 2013. ,
Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria, J Bacteriol, vol.191, issue.8, pp.2501-2511, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00400283
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006. ,
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments, Nucleic Acids Res, vol.34, pp.609-612, 2006. ,
Phylogenetic modelling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proc Natl Acad Sci U S A, vol.109, issue.43, pp.17513-17518, 2012. ,
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths, PLoS Genet, vol.5, issue.1, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00390293
MicroScope: a platform for microbial genome annotation and comparative genomics, Database, issue.0, p.21, 2009. ,
MicroScope: an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data, Nucleic Acids Res, vol.41, pp.636-647, 2013. ,
Characterization of a Brucella species 25-kilobase DNA fragment deleted from Brucella abortus reveals a large gene cluster related to the synthesis of a polysaccharide, Infect Immun, vol.69, issue.11, pp.6738-6748, 2001. ,
Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil, Appl Environ Microbiol, vol.69, issue.3, pp.1482-1487, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-00427492
Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid, J Biotechnol, vol.155, issue.1, pp.50-62, 2011. ,
Quantifying homologous replacement of loci between haloarchaeal species, Genome Biol Evol, vol.4, issue.12, pp.1223-1244, 2012. ,
The genome of the natural genetic engineer Agrobacterium tumefaciens C58, Science, vol.294, issue.5550, pp.2317-2323, 2001. ,
The genome of Rhizobium leguminosarum has recognizable core and accessory components, Genome Biol, vol.7, issue.4, 2006. ,