N. El-mabrouk and D. Sankoff, Analysis of Gene Order Evolution Beyond Single-Copy Genes, Methods Mol. Biol, vol.855, pp.397-429, 2012.
DOI : 10.1007/978-1-61779-582-4_15

F. S. Dietrich, S. Voegeli, S. Brachat, A. Lerch, K. Gates et al., The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome, Science, vol.304, issue.5668, pp.304-307, 2004.
DOI : 10.1126/science.1095781

B. Dujon, D. Sherman, G. Fischer, P. Durrens, S. Casaregola et al., Genome evolution in yeasts, Nature, vol.316, issue.6995, pp.35-44, 2004.
DOI : 10.1093/nar/gkg056

URL : https://hal.archives-ouvertes.fr/hal-00104411

C. Soderlund, M. Bomhoff, and W. M. Nelson, SyMAP v3.4: a turnkey synteny system with application to plant genomes, Nucleic Acids Research, vol.39, issue.10, p.68, 2011.
DOI : 10.1093/nar/gkr123

M. Huynen, B. Snel, W. Lathe, . Iii, and P. Bork, Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences, Genome Research, vol.10, issue.8, pp.1204-1210, 2000.
DOI : 10.1101/gr.10.8.1204

X. H. Zheng, F. Lu, Z. Y. Wang, F. Zhong, J. Hoover et al., Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs, Bioinformatics, vol.21, issue.6, pp.703-710, 2005.
DOI : 10.1093/bioinformatics/bti045

T. Doerks, C. Von-mering, and P. Bork, Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes, Nucleic Acids Research, vol.32, issue.21, pp.6321-6326, 2004.
DOI : 10.1093/nar/gkh973

E. M. Zdobnov, M. Campillos, E. D. Harrington, D. Torrents, and P. Bork, Protein coding potential of retroviruses and other transposable elements in vertebrate genomes, Nucleic Acids Research, vol.33, issue.3, pp.946-954, 2005.
DOI : 10.1093/nar/gki236

T. Dandekar, B. Snel, M. Huynen, and P. Bork, Conservation of gene order: a fingerprint of proteins that physically interact, Trends in Biochemical Sciences, vol.23, issue.9, pp.324-328, 1998.
DOI : 10.1016/S0968-0004(98)01274-2

R. Overbeek, M. Fonstein, M. Souza, G. D. Pusch, and N. Maltsev, The use of gene clusters to infer functional coupling, Proceedings of the National Academy of Sciences, vol.96, issue.6, pp.2896-2901, 1999.
DOI : 10.1073/pnas.96.6.2896

J. Tamames, G. Casari, C. Ouzounis, and A. Valencia, Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes, Journal of Molecular Evolution, vol.372, issue.1, pp.66-73, 1997.
DOI : 10.1007/PL00006122

C. Rodelsperger, G. Guo, M. Kolanczyk, A. Pletschacher, S. Kohler et al., Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions, Nucleic Acids Research, vol.39, issue.7, pp.2492-2502, 2011.
DOI : 10.1093/nar/gkq1081

P. J. Roy, J. M. Stuart, J. Lund, and S. K. Kim, Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans, Nature, vol.418, pp.975-979, 2002.

F. Enault, K. Suhre, and J. M. Claverie, Phydbac " Gene Function Predictor " : a gene annotation tool based on genomic context analysis, BMC Bioinformatics, vol.6, issue.1, pp.247-257, 2005.
DOI : 10.1186/1471-2105-6-247

J. Lehmann, P. F. Stadler, and S. J. Prohaska, SynBlast: Assisting the analysis of conserved synteny information, BMC Bioinformatics, vol.9, issue.1, pp.351-365, 2008.
DOI : 10.1186/1471-2105-9-351

T. D. Otto, G. P. Dillon, W. S. Degrave, and M. Berriman, RATT: Rapid Annotation Transfer Tool, Nucleic Acids Research, vol.39, issue.9, p.57, 2011.
DOI : 10.1093/nar/gkq1268

R. Overbeek, N. Larsen, T. Walunas, M. Souza, G. Pusch et al., The ERGOTM genome analysis and discovery system, Nucleic Acids Research, vol.31, issue.1, pp.164-171, 2003.
DOI : 10.1093/nar/gkg148

D. Vallenet, L. Labarre, Z. Rouy, V. Barbe, S. Bocs et al., MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2006.
DOI : 10.1093/nar/gkj406

A. P. Yelton, B. C. Thomas, S. L. Simmons, P. Wilmes, A. Zemla et al., A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes, PLoS Computational Biology, vol.47, issue.10, p.1002230, 2011.
DOI : 10.1371/journal.pcbi.1002230.s012

G. Bourque, P. A. Pevzner, and G. Tesler, Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes, Genome Research, vol.14, issue.4, pp.507-516, 2004.
DOI : 10.1101/gr.1975204

A. G. Clark, M. B. Eisen, D. R. Smith, C. M. Bergman, B. Oliver et al., Evolution of genes and genomes on the Drosophila phylogeny, Nature, vol.2, issue.7167, pp.203-218, 2007.
DOI : 10.1038/nature06341

J. Ma, L. Zhang, B. B. Suh, B. J. Raney, R. C. Burhans et al., Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, issue.12, pp.1557-1565, 2006.
DOI : 10.1101/gr.5383506

J. Tamames, Evolution of gene order conservation in prokaryotes, Genome Biol, vol.2, pp.20-0020, 2001.

H. Kikuta, M. Laplante, P. Navratilova, A. Z. Komisarczuk, P. G. Engstrom et al., Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates, Genome Research, vol.17, issue.5, 2007.
DOI : 10.1101/gr.6086307

URL : https://hal.archives-ouvertes.fr/hal-00189979

W. J. Murphy, D. M. Larkin, A. Everts-van-der-wind, G. Bourque, G. Tesler et al., Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps, Science, vol.309, issue.5734, pp.613-617, 2005.
DOI : 10.1126/science.1111387

P. Pevzner and G. Tesler, Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes, Genome Research, vol.13, issue.1, 2003.
DOI : 10.1101/gr.757503

D. Boffelli, M. A. Nobrega, and E. M. Rubin, Comparative genomics at the vertebrate extremes, Nature Reviews Genetics, vol.129, issue.6, pp.456-465, 2004.
DOI : 10.1016/S0378-1119(02)00592-9

E. Hunt, N. Hanlon, D. P. Leader, H. Bryce, and A. F. Dominiczak, The Visual Language of Synteny, OMICS: A Journal of Integrative Biology, vol.8, issue.4, pp.289-305, 2004.
DOI : 10.1089/omi.2004.8.289

C. B. Nielsen, M. Cantor, I. Dubchak, D. Gordon, and T. Wang, Visualizing genomes: techniques and challenges, Nature Methods, vol.25, issue.3s, pp.5-15, 2010.
DOI : 10.1038/nmeth.1422

C. Rodelsperger and C. Dieterich, CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes, PLoS ONE, vol.5, issue.1, p.8861, 2010.
DOI : 10.1371/journal.pone.0008861.s015

B. J. Haas, A. L. Delcher, J. R. Wortman, and S. L. Salzberg, DAGchainer: a tool for mining segmental genome duplications and synteny, Bioinformatics, vol.20, issue.18, pp.3643-3646, 2004.
DOI : 10.1093/bioinformatics/bth397

P. P. Calabrese, S. Chakravarty, and T. J. Vision, Fast identification and statistical evaluation of segmental homologies in comparative maps, Bioinformatics, vol.19, issue.Suppl 1, pp.74-80, 2003.
DOI : 10.1093/bioinformatics/btg1008

S. Proost, J. Fostier, D. De-witte, B. Dhoedt, P. Demeester et al., i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets, Nucleic Acids Research, vol.40, issue.2, p.11
DOI : 10.1093/nar/gkr955

A. U. Sinha and J. Meller, Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms, BMC Bioinformatics, vol.8, issue.1, pp.82-91, 2007.
DOI : 10.1186/1471-2105-8-82

M. P. Ng, I. A. Vergara, C. Frech, Q. Chen, X. Zeng et al., OrthoClusterDB: an online platform for synteny blocks, BMC Bioinformatics, vol.10, issue.1, pp.192-200, 2009.
DOI : 10.1186/1471-2105-10-192

F. Guyon, G. Vaysseix, and E. Barillot, MAPPETSHOW: NON-LINEAR VISUALIZATION FOR GENOME DATA, Biocomputing 2000, pp.206-217, 2000.
DOI : 10.1142/9789814447331_0020

T. Davidsen, E. Beck, A. Ganapathy, R. Montgomery, N. Zafar et al., The comprehensive microbial resource, Nucleic Acids Research, vol.38, issue.Database, pp.340-345, 2010.
DOI : 10.1093/nar/gkp912

K. E. Nelson, D. E. Fouts, E. F. Mongodin, J. Ravel, R. T. Deboy et al., Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species, Nucleic Acids Research, vol.32, issue.8, pp.2386-2395, 2004.
DOI : 10.1093/nar/gkh562

T. D. Read, G. S. Myers, R. C. Brunham, W. C. Nelson, I. T. Paulsen et al., Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae, Nucleic Acids Research, vol.31, issue.8, pp.2134-2147, 2003.
DOI : 10.1093/nar/gkg321

M. J. Richards, J. R. Edwards, D. H. Culver, and R. P. Gaynes, Conclusions:, Infection Control & Hospital Epidemiology, vol.144, issue.08, pp.510-515, 2000.
DOI : 10.1086/501639

B. D. Jett, M. M. Huycke, and M. S. Gilmore, Virulence of enterococci., Clinical Microbiology Reviews, vol.7, issue.4, pp.462-478, 1994.
DOI : 10.1128/CMR.7.4.462

I. T. Paulsen, L. Banerjei, G. S. Myers, K. E. Nelson, R. Seshadri et al., Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis, Science, vol.299, issue.5615, pp.2071-2074, 2003.
DOI : 10.1126/science.1080613

R. C. Matos, N. Lapaque, L. Rigottier-gois, L. Debarbieux, T. Meylheuc et al., Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits, PLoS Genetics, vol.7, issue.6, p.1003539, 2013.
DOI : 10.1371/journal.pgen.1003539.s007

URL : https://hal.archives-ouvertes.fr/hal-01190746

I. Pagani, K. Liolios, J. Jansson, I. M. Chen, T. Smirnova et al., The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata, Nucleic Acids Research, vol.40, issue.D1, pp.571-579, 2012.
DOI : 10.1093/nar/gkr1100

S. M. Mcbride, V. A. Fischetti, D. J. Leblanc, R. C. Moellering, . Jr et al., Genetic Diversity among Enterococcus faecalis, PLoS ONE, vol.178, issue.3, p.582, 2007.
DOI : 10.1371/journal.pone.0000582.s003

M. Solheim, M. C. Brekke, L. G. Snipen, R. J. Willems, I. F. Nes et al., Comparative genomic analysis reveals significant enrichment of mobile genetic elements and genes encoding surface structure-proteins in hospital, 2011.

A. Bourgogne, D. A. Garsin, X. Qin, K. V. Singh, J. Sillanpaa et al., Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF, Genome Biology, vol.9, issue.7, pp.110-126, 2008.
DOI : 10.1186/gb-2008-9-7-r110

F. Reffuveille, C. Leneveu, S. Chevalier, Y. Auffray, and A. Rincé, Lipoproteins of Enterococcus faecalis: bioinformatic identification, expression analysis and relation to virulence, Microbiology, vol.157, issue.11, pp.3001-3013, 2011.
DOI : 10.1099/mic.0.053314-0

URL : https://hal.archives-ouvertes.fr/hal-00741326

I. G. Sava, E. Heikens, and J. Huebner, Pathogenesis and immunity in enterococcal infections, Clinical Microbiology and Infection, vol.16, issue.6, pp.533-540, 2010.
DOI : 10.1111/j.1469-0691.2010.03213.x

X. Zhang, J. Top, M. De-been, D. Bierschenk, M. Rogers et al., Identification of a Genetic Determinant in Clinical Enterococcus faecium Strains That Contributes to Intestinal Colonization During Antibiotic Treatment, Journal of Infectious Diseases, vol.207, issue.11, pp.1780-1786, 2013.
DOI : 10.1093/infdis/jit076

E. R. Hondorp, S. C. Hou, L. L. Hause, K. Gera, C. E. Lee et al., PTS phosphorylation of Mga modulates regulon expression and virulence in the group A streptococcus, Molecular Microbiology, vol.102, issue.Part 9, pp.1176-1193, 2013.
DOI : 10.1111/mmi.12250

M. C. Wu, Y. C. Chen, T. L. Lin, P. F. Hsieh, and J. T. Wang, Cellobiose-Specific Phosphotransferase System of Klebsiella pneumoniae and Its Importance in Biofilm Formation and Virulence, Infection and Immunity, vol.80, issue.7, pp.2464-2472, 2012.
DOI : 10.1128/IAI.06247-11

Y. Maruyama, Y. Nakamichi, T. Itoh, B. Mikami, W. Hashimoto et al., Substrate Specificity of Streptococcal Unsaturated Glucuronyl Hydrolases for Sulfated Glycosaminoglycan, Journal of Biological Chemistry, vol.284, issue.27, pp.18059-18069, 2009.
DOI : 10.1074/jbc.M109.005660

M. S. Poptsova and J. P. Gogarten, Using comparative genome analysis to identify problems in annotated microbial genomes, Microbiology, vol.156, issue.7, pp.1909-1917, 2010.
DOI : 10.1099/mic.0.033811-0

S. E. Brenner, Errors in genome annotation, Trends in Genetics, vol.15, issue.4, pp.132-133, 1999.
DOI : 10.1016/S0168-9525(99)01706-0

D. Devos and A. Valencia, Intrinsic errors in genome annotation, Trends in Genetics, vol.17, issue.8, pp.429-431, 2001.
DOI : 10.1016/S0168-9525(01)02348-4

C. E. Jones, A. L. Brown, and U. Baumann, Estimating the annotation error rate of curated GO database sequence annotations, BMC Bioinformatics, vol.8, issue.1, pp.170-179, 2007.
DOI : 10.1186/1471-2105-8-170

L. Sui, J. C. Warren, J. P. Russell, and N. V. Stourman, Comparison of the functions of glutathionylspermidine synthetase/amidase from E. coli and its predicted homologues YgiC and YjfC, Int. J. Biochem. Mol. Biol, vol.3, pp.302-312, 2012.

O. 'donoghue, S. I. Gavin, A. C. Gehlenborg, N. Goodsell, D. S. Heriche et al., Visualizing biological data???now and in the future, Nature Methods, vol.25, issue.3s, pp.2-4, 2010.
DOI : 10.1038/nmeth.f.301

K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou et al., AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system, Nucleic Acids Research, vol.34, issue.12, pp.3533-3545, 2006.
DOI : 10.1093/nar/gkl471