Origin of an Alternative Genetic Code in the Extremely Small and GC???Rich Genome of a Bacterial Symbiont, PLoS Genetics, vol.4, issue.7, 2009. ,
DOI : 10.1371/journal.pgen.1000565.s003
Complete genome sequence of the myxobacterium Sorangium cellulosum, Nature Biotechnology, vol.34, issue.11, pp.1281-1289, 2007. ,
DOI : 10.1038/nbt1354
The Role of Domain Redundancy in Genetic Robustness Against Null Mutations, Journal of Molecular Biology, vol.362, issue.2, pp.184-191, 2006. ,
DOI : 10.1016/j.jmb.2006.07.033
Evolution of protein complexes by duplication of homomeric interactions, Genome Biology, vol.8, issue.4, p.51, 2007. ,
DOI : 10.1186/gb-2007-8-4-r51
Gene duplications, robustness and evolutionary innovations, BioEssays, vol.313, issue.4, pp.367-373, 2008. ,
DOI : 10.1002/bies.20728
URL : http://www.zora.uzh.ch/3744/2/Wagner_Bioessays_2008V.pdf
An adaptive radiation model for the origin of new gene functions, Nature Genetics, vol.50, issue.6, pp.573-577, 2005. ,
DOI : 10.1038/ng1579
Multiple pathways of selected gene amplification during adaptive mutation, Proceedings of the National Academy of Sciences, vol.103, issue.46, pp.17319-17324, 2006. ,
DOI : 10.1073/pnas.0608309103
Gene Amplification and Adaptive Evolution in Bacteria, Annual Review of Genetics, vol.43, issue.1, pp.167-195, 2009. ,
DOI : 10.1146/annurev-genet-102108-134805
Turning a hobby into a job: How duplicated genes find new functions, Nature Reviews Genetics, vol.26, issue.12, pp.938-950, 2008. ,
DOI : 10.1038/nrg2482
Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol.22, issue.1, pp.58-73, 2007. ,
DOI : 10.1002/jez.b.21124
The life and death of gene families, BioEssays, vol.105, issue.1, pp.29-39, 2009. ,
DOI : 10.1002/bies.080085
The evolution of gene duplications: classifying and distinguishing between models, Nature Reviews Genetics, vol.178, issue.4, pp.97-108, 2010. ,
DOI : 10.1038/nrg2689
The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation, PLoS Computational Biology, vol.188, issue.11, 2006. ,
DOI : 10.1371/journal.pcbi.0020143.st001
Evolution by leaps: gene duplication in bacteria, Biology Direct, vol.4, issue.1, p.46, 2009. ,
DOI : 10.1186/1745-6150-4-46
Genesis, effects and fates of repeats in prokaryotic genomes, FEMS Microbiology Reviews, vol.33, issue.3, pp.539-571, 2009. ,
DOI : 10.1111/j.1574-6976.2009.00169.x
The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host cell interaction genes, Proceedings of the National Academy of Sciences, vol.104, issue.19, pp.7981-7986, 2007. ,
DOI : 10.1073/pnas.0611553104
Evolution of sensory complexity recorded in a myxobacterial genome, Proceedings of the National Academy of Sciences, vol.103, issue.41, pp.15200-15205, 2006. ,
DOI : 10.1073/pnas.0607335103
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse, Proceedings of the National Academy of Sciences, vol.103, issue.42, pp.15582-15587, 2006. ,
DOI : 10.1073/pnas.0607048103
Genome Rearrangements, Deletions, and Amplifications in the Natural Population of Bartonella henselae, Journal of Bacteriology, vol.188, issue.21, pp.7426-7439, 2006. ,
DOI : 10.1128/JB.00472-06
Conservation and topology of protein interaction networks under duplication-divergence evolution, Proceedings of the National Academy of Sciences, vol.105, issue.29, pp.9863-9868, 2008. ,
DOI : 10.1073/pnas.0804119105
Gene regulatory network growth by duplication, Nature Genetics, vol.36, issue.5, pp.492-496, 2004. ,
DOI : 10.1038/ng1340
Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, issue.6784, pp.299-304, 2000. ,
DOI : 10.1038/35012500
Evolutionary Origins of Genomic Repertoires in Bacteria, PLoS Biology, vol.269, issue.5, 2005. ,
DOI : 10.1371/journal.pbio.0030130.t001
URL : https://hal.archives-ouvertes.fr/hal-00427770
Prokaryotic Evolution in Light of Gene Transfer, Molecular Biology and Evolution, vol.19, issue.12, pp.2226-2238, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004046
Comparative genomics: the bacterial pan-genome, Current Opinion in Microbiology, vol.11, issue.5, pp.472-477, 2008. ,
DOI : 10.1016/j.mib.2008.09.006
The Balance of Driving Forces During Genome Evolution in Prokaryotes, Genome Research, vol.13, issue.7, pp.1589-1594, 2003. ,
DOI : 10.1101/gr.1092603
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
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution, Proceedings of the National Academy of Sciences, vol.105, issue.29, pp.10039-10044, 2008. ,
DOI : 10.1073/pnas.0800679105
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
Duplication is more common among laterally transferred genes than among indigenous genes, Genome Biology, vol.4, issue.8, p.48, 2003. ,
DOI : 10.1186/gb-2003-4-8-r48
Gene duplication and biased functional retention of paralogs in bacterial genomes, Trends in Microbiology, vol.12, issue.4, pp.148-154, 2004. ,
DOI : 10.1016/j.tim.2004.02.007
Comparative genomics of genefamily size in closely related bacteria, Genome Biology, vol.5, issue.4, p.27, 2004. ,
DOI : 10.1186/gb-2004-5-4-r27
Bayesian Estimation of Ancestral Character States on Phylogenies, Systematic Biology, vol.53, issue.5, pp.673-684, 2004. ,
DOI : 10.1080/10635150490522232
Periodic Extinctions of Transposable Elements in Bacterial Lineages: Evidence from Intragenomic Variation in Multiple Genomes, Molecular Biology and Evolution, vol.23, issue.4, pp.723-733, 2006. ,
DOI : 10.1093/molbev/msj085
Causes of Insertion Sequences Abundance in Prokaryotic Genomes, Molecular Biology and Evolution, vol.24, issue.4, pp.969-981, 2007. ,
DOI : 10.1093/molbev/msm014
The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli, PLoS Computational Biology, vol.22, issue.4, 2008. ,
DOI : 10.1371/journal.pcbi.1000059.s007
Evolutionary patterns in prokaryotic genomes, Current Opinion in Microbiology, vol.11, issue.5, pp.454-460, 2008. ,
DOI : 10.1016/j.mib.2008.09.007
GENE AMPLIFICATION AND GENOMIC PLASTICITY IN PROKARYOTES, Annual Review of Genetics, vol.31, issue.1, pp.91-111, 1997. ,
DOI : 10.1146/annurev.genet.31.1.91
Origin and fate of repeats in bacteria, Nucleic Acids Research, vol.30, issue.13, pp.2987-2994, 2002. ,
DOI : 10.1093/nar/gkf391
Molecular models accounting for the gene conversion reactions mediating gonococcal pilin antigenic variation, Molecular Microbiology, vol.89, issue.5, pp.1146-1158, 2000. ,
DOI : 10.1016/S0092-8674(00)80206-8
Extensive repetitive DNA facilitates prokaryotic genome plasticity, Proceedings of the National Academy of Sciences, vol.100, issue.23, pp.13579-13584, 2003. ,
DOI : 10.1073/pnas.1735481100
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC263856
Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age, Proceedings of the National Academy of Sciences, vol.98, issue.26, pp.15056-15061, 2001. ,
DOI : 10.1073/pnas.251396098
Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences, Proceedings of the National Academy of Sciences, vol.98, issue.1, pp.182-187, 2001. ,
DOI : 10.1073/pnas.98.1.182
The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Research, vol.15, issue.3, pp.1281-1295, 1987. ,
DOI : 10.1093/nar/15.3.1281
Unbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants, Molecular & Cellular Proteomics, vol.8, issue.12, pp.2770-2777, 2009. ,
DOI : 10.1074/mcp.M900240-MCP200
How Common Are Intragene Windows with K A > K S Owing to Purifying Selection on Synonymous Mutations?, Journal of Molecular Evolution, vol.101, issue.6, pp.646-655, 2007. ,
DOI : 10.1007/s00239-006-0207-7
Amelioration of Bacterial Genomes: Rates of Change and Exchange, Journal of Molecular Evolution, vol.44, issue.4, pp.383-397, 1997. ,
DOI : 10.1007/PL00006158
Genetic flux over time in the Salmonella lineage, Genome Biology, vol.8, issue.6, p.100, 2007. ,
DOI : 10.1186/gb-2007-8-6-r100
An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins, Molecular Biology and Evolution, vol.21, issue.1, pp.108-116, 2004. ,
DOI : 10.1093/molbev/msh004
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins, PLoS Biology, vol.22, issue.4, 2009. ,
DOI : 10.1371/journal.pbio.1000096.st018
New insights into the regulatory networks of paralogous genes in bacteria, Microbiology, vol.156, issue.1, pp.14-22, 2010. ,
DOI : 10.1099/mic.0.033266-0
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli, Genome Biology, vol.9, issue.1, p.4, 2008. ,
DOI : 10.1186/gb-2008-9-1-r4
Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years, Molecular Biology and Evolution, vol.25, issue.3, pp.559-567, 2008. ,
DOI : 10.1093/molbev/msm283
The impact of long-distance horizontal gene transfer on prokaryotic genome size, Proceedings of the National Academy of Sciences, vol.106, issue.51, pp.21748-21753, 2009. ,
DOI : 10.1073/pnas.0907584106
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer, Science, vol.318, issue.5855, pp.1449-1452, 2007. ,
DOI : 10.1126/science.1147112
URL : http://escholarship.org/uc/item/14d6g2w5.pdf
Genetic flux over time in the Salmonella lineage, Genome Biology, vol.8, issue.6, p.100, 2007. ,
DOI : 10.1186/gb-2007-8-6-r100
On the need for widespread horizontal gene transfers under genome size constraint, Biology Direct, vol.4, issue.1, p.28, 2009. ,
DOI : 10.1186/1745-6150-4-28
Inference and Analysis of the Relative Stability of Bacterial Chromosomes, Molecular Biology and Evolution, vol.23, issue.3, pp.513-522, 2006. ,
DOI : 10.1093/molbev/msj052
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer, Nature Genetics, vol.428, issue.12, pp.1372-1375, 2005. ,
DOI : 10.1038/ng1686
Erosion of interaction networks in reduced and degraded genomes, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol.14, issue.1, pp.97-103, 2007. ,
DOI : 10.1002/jez.b.21147
Complexity, connectivity, and duplicability as barriers to lateral gene transfer, Genome Biology, vol.8, issue.8, p.156, 2007. ,
DOI : 10.1186/gb-2007-8-8-r156
Horizontal gene transfer in eukaryotic evolution, Nature Reviews Genetics, vol.320, issue.8, pp.605-618, 2008. ,
DOI : 10.1038/nrg2386
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features, Proceedings of the National Academy of Sciences, vol.103, issue.31, pp.11647-11652, 2006. ,
DOI : 10.1073/pnas.0604795103
URL : https://hal.archives-ouvertes.fr/hal-00164247
The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, vol.9, issue.7219, pp.239-244, 2008. ,
DOI : 10.1038/nature07410
URL : https://hal.archives-ouvertes.fr/cea-00910244
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research, vol.30, issue.7, pp.1575-1584, 2002. ,
DOI : 10.1093/nar/30.7.1575
ISfinder: the reference centre for bacterial insertion sequences, Nucleic Acids Research, vol.34, issue.90001, pp.32-36, 2006. ,
DOI : 10.1093/nar/gkj014
URL : https://hal.archives-ouvertes.fr/hal-00021179
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic Acids Research, vol.34, issue.20, pp.5839-5851, 2006. ,
DOI : 10.1093/nar/gkl732
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, issue.2, pp.180-189, 2009. ,
DOI : 10.1109/TCBB.2009.9
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003. ,
DOI : 10.1101/gr.1224503
Similar compositional biases are caused by very different mutational effects, Genome Research, vol.16, issue.12, pp.1537-1547, 2006. ,
DOI : 10.1101/gr.5525106
Detecting laterally transferred genes: use of entropic clustering methods and genome position, Nucleic Acids Research, vol.35, issue.14, pp.4629-4639, 2007. ,
DOI : 10.1093/nar/gkm204
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
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
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997. ,
DOI : 10.1093/oxfordjournals.molbev.a025808
URL : https://hal.archives-ouvertes.fr/lirmm-00730410
PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-556, 1997. ,
DOI : 10.1093/bioinformatics/13.5.555