Biased biological functions of horizontally transferred genes in prokaryotic genomes, Nature Genet, vol.36, pp.760-766, 2004. ,
Reconciling the many faces of lateral gene transfer, Trends Microbiol, vol.10, pp.1-4, 2002. ,
On the track of natural transformation in soil, FEMS Microb Ecol, vol.15, pp.109-117, 1994. ,
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution, Nucleic Acids Res, vol.29, pp.3742-3756, 2001. ,
Genetic barriers among bacteria, Trends Microbiol, vol.4, pp.69-72, 1996. ,
Homeologous recombination and mismatch repair during transformation in Streptococcus pneumoniae: saturation of the Hex mismatch repair system, Proc Natl Acad Sci U S A, vol.92, pp.9052-9056, 1995. ,
Prokaryotic diversity-magnitude, dynamics, and controlling factors, Science, vol.296, pp.1064-1066, 2002. ,
Detection of lateral gene transfer among microbial genomes, Curr Opin Genet Dev, vol.11, pp.620-626, 2001. ,
Genome sequence of the plant pathogen Ralstonia solanacearum, Nature, vol.415, pp.497-502, 2002. ,
URL : https://hal.archives-ouvertes.fr/hal-00427300
During infection of its host, the plant pathogen Ralstonia solanacearum naturally develops a state of competence and exchanges genetic material, molecular plant-microbe interact, vol.12, pp.467-672, 1999. ,
The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme, Proc R Soc Lond B Biol Sci, vol.205, pp.581-598, 1979. ,
Evidence for the adaptive evolution of mutation rates, Cell, vol.101, pp.581-584, 2000. ,
The source of laterally transferred genes in bacterial genomes, Genome Biol, vol.4, p.57, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-00427389
G+C3 Structuring along the genome: A common feature in prokaryotes, Mol Biol Evol, vol.20, pp.471-483, 2003. ,
URL : https://hal.archives-ouvertes.fr/hal-00427485
Molecular archaeology of the Escherichia coli genome, Proc Natl Acad Sci, vol.95, pp.9413-9417, 1998. ,
Base composition bias might result from competition for metabolic resources, Trends Genet, vol.18, pp.291-294, 2002. ,
The codon Adaptation Index: a measure of directional synonymous codon usage bias, and its potential applications, Nucl Acids Res, vol.15, pp.1281-1295, 1987. ,
Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis, J Bacteriol, vol.189, pp.377-387, 2007. ,
Goodness-of-fit tests on a circle, Biometrika, vol.48, pp.109-114, 1961. ,
Role of the Escherichia coli recombination hotspot, Chi, in RecABCD-dependent homologous pairing, J Biol Chem, vol.270, pp.16360-16370, 1995. ,
Very short patch repair: reducing the cost of cytosine methylation, Mol Microbiol, vol.20, pp.467-473, 1996. ,
The vsr gene product of E. coli K-12 is a strand-and sequence-specific DNA mismatch endonuclease, Nature, vol.353, pp.776-778, 1991. ,
Role of the Multidrug Efflux Systems of Pseudomonas aeruginosa in Organic Solvent Tolerance, J Bacteriol, vol.180, pp.2987-2991, 1998. ,
The pilA regulatory gene modulates the pilus-mediated adhesion of Neisseria meningitidis by controlling the transcription of pilC1, Mol Microbiol, vol.19, pp.1073-1084, 1996. ,
Bacterial Wilt: The Disease and its causative agent, Pseudomonas solanacearum, CAB INTERNATIONAL, pp.9-24, 1994. ,
Opportunistic colonization of Ralstonia solanacearum-infected plants by Acinetobacter sp. and its natural competence development, Microb Ecol, vol.43, pp.291-297, 2002. ,
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium, Proc Natl Acad Sci, vol.99, pp.9509-9514, 2002. ,
Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen, Nature, vol.406, pp.959-964, 2000. ,
Regulation of stalk elongation by phosphate in Caulobacter crescentus, J Bacteriol, vol.182, pp.337-347, 2000. ,
Complete genome sequence of Caulobacter crescentus, Proc Natl Acad Sci, vol.98, pp.4136-4141, 2001. ,
Conditions for natural transformation of Ralstonia solanacearum, Appl Environ Microbiol, vol.63, pp.4965-4968, 1997. ,
URL : https://hal.archives-ouvertes.fr/hal-02686008
DNA as a nutrient: novel role for bacterial competence gene homologs, J Bacteriol, vol.183, pp.6288-6293, 2001. ,
Genome dynamics of short oligonucleotides: The example of bacterial DNA uptake enhancing sequences, PLoS ONE, vol.741, pp.1-15, 2007. ,
Characteristics of Chi distribution on different bacterial genomes, Res Microbiol, vol.150, pp.579-587, 1999. ,
URL : https://hal.archives-ouvertes.fr/hal-02697692
Biochemistry of homologous recombination in Escherichia coli, Microbiol Rev, vol.58, pp.401-465, 1994. ,
Cellular response to horizontally transferred DNA in Escherichia coli is tuned by DNA repair systems, DNA Repair (Amst), vol.4, pp.221-229, 2005. ,
Horizontal gene transfer, genome innovation and evolution, Nat Rev Microbiol, vol.3, pp.679-687, 2005. ,
Phenotypic characterization and deoxyribonucleic acid homologies of Pseudomonas solanacearum, J Bacteriol, vol.107, pp.690-696, 1971. ,
Genomics and the bacterial species problem, Genome Biol, vol.7, p.116, 2006. ,
Phylogenetic evidence for horizontal transfer of mutS alleles among naturally occurring Escherichia coli strains, J Bacteriol, vol.183, pp.1631-1644, 2001. ,
Evolutionary implications of the frequent horizontal transfer of mismatch repair genes, Cell, vol.103, pp.711-721, 2000. ,
Virulence genes are carried by a megaplasmid of the plant pathogen Pseudomonas solanacearum, Mol Gen Genet, vol.205, pp.270-275, 1986. ,
URL : https://hal.archives-ouvertes.fr/hal-02727506
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004. ,
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol Microbiol, vol.17, pp.540-552, 2000. ,
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst Biol, vol.52, pp.696-704, 2003. ,
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach, Mol Biol Evol, vol.18, pp.691-699, 2001. ,
Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Mo Biol Evol, vol.16, pp.1114-1116, 1999. ,
Genes for gentamicin-(3)-N-acetyltransferases III and IV: I. Nucleotide sequence of the AAC(3)-IV gene and possible involvement of an IS140 element in its expression, Mol Gen Genet, vol.193, pp.179-187, 1984. ,
SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis, Structural approaches to sequence evolution: Molecules, networks, populations Springer Verlag: Biological and Medical Physics, pp.207-232, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00434576