P. López-garcía, Y. Zivanovic, P. Deschamps, and D. Moreira, Bacterial gene import and mesophilic adaptation in archaea, Nature Reviews Microbiology, vol.5, issue.7, pp.447-56, 2015.
DOI : 10.1016/j.bbamem.2013.06.023

W. Grant, Life at low water activity, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.359, issue.1448, pp.1249-67, 2004.
DOI : 10.1098/rstb.2004.1502

M. Roesser and V. Müller, Osmoadaptation in bacteria and archaea: common principles and differences, Environmental Microbiology, vol.217, issue.12, pp.743-54, 2001.
DOI : 10.1126/science.7112124

S. Kennedy, W. Ng, S. Salzberg, L. Hood, and S. Dassarma, Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence, Genome Research, vol.11, issue.10, pp.1641-50, 2001.
DOI : 10.1101/gr.190201

S. Nelson-sathi, T. Dagan, G. Landan, A. Janssen, M. Steel et al., Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea, Proceedings of the National Academy of Sciences, vol.4, issue.4, 2012.
DOI : 10.1093/bioinformatics/btr088

S. Nelson-sathi, F. Sousa, M. Roettger, N. Lozada-chávez, T. Thiergart et al., Origins of major archaeal clades correspond to gene acquisitions from bacteria, Nature, vol.21, issue.7532, pp.77-80, 2015.
DOI : 10.1093/bioinformatics/bti191

M. Groussin, B. Boussau, G. Szöllõsi, L. Eme, M. Gouy et al., Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated, Molecular Biology and Evolution, vol.517, issue.2, pp.305-315, 2016.
DOI : 10.1093/sysbio/syt054

URL : https://hal.archives-ouvertes.fr/hal-01913926

E. Becker, P. Seitzer, A. Tritt, D. Larsen, M. Krusor et al., Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response, PLoS Genetics, vol.13, issue.11, p.1004784, 2014.
DOI : 10.1371/journal.pgen.1004784.s052

T. Williams, G. Szöll?si, A. Spang, P. Foster, S. Heaps et al., Integrative modeling of gene and genome evolution roots the archaeal tree of life, Proceedings of the National Academy of Sciences, vol.517, issue.23, pp.4602-4613, 2017.
DOI : 10.18637/jss.v022.i04

Z. Blount, J. Barrick, C. Davidson, and R. Lenski, Genomic analysis of a key innovation in an experimental Escherichia coli population, Nature, vol.1, issue.7417, pp.513-521, 2012.
DOI : 10.1016/S0378-1119(03)00585-7

M. Toll-riera, S. Millan, A. Wagner, A. Maclean, and R. , The Genomic Basis of Evolutionary Innovation in Pseudomonas aeruginosa, PLOS Genetics, vol.421, issue.6918, p.1006005, 2016.
DOI : 10.1371/journal.pgen.1006005.s016

A. Mclysaght and L. Hurst, Open questions in the study of de novo genes: what, how and why, Nature Reviews Genetics, vol.57, issue.9, pp.567-78, 2016.
DOI : 10.1002/pros.20685

D. Andersson, J. Jerlström-hultqvist, and J. Näsvall, Evolution of New Functions De Novo and from Preexisting Genes, Cold Spring Harbor Perspectives in Biology, vol.7, issue.6, p.17996, 2015.
DOI : 10.1101/cshperspect.a017996

S. Chen, B. Krinsky, and M. Long, New genes as drivers of phenotypic evolution, Nature Reviews Genetics, vol.164, issue.9, pp.645-60, 2013.
DOI : 10.1534/genetics.110.119446

S. Pasek, J. Risler, and P. Brézellec, Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins, Bioinformatics, vol.3, issue.5, pp.1418-1441, 2006.
DOI : 10.1186/gb-2002-3-5-research0024

V. Merhej, C. Notredame, M. Royer-carenzi, P. Pontarotti, and D. Raoult, The Rhizome of Life: The Sympatric Rickettsia felis Paradigm Demonstrates the Random Transfer of DNA Sequences, Molecular Biology and Evolution, vol.51, issue.2, pp.3213-3236, 2011.
DOI : 10.1186/gb-2007-8-8-r156

URL : https://hal.archives-ouvertes.fr/hal-01105200

C. Chan, R. Beiko, and M. Ragan, Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements, Journal of Bacteriology, vol.193, issue.15, pp.3964-77, 2011.
DOI : 10.1128/JB.01524-10

R. Méheust, E. Zelzion, D. Bhattacharya, P. Lopez, and E. Bapteste, Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis, Proceedings of the National Academy of Sciences, vol.517, issue.7532, pp.3579-84, 2016.
DOI : 10.1093/bioinformatics/btu033

P. Jachiet, R. Pogorelcnik, A. Berry, P. Lopez, and E. Bapteste, MosaicFinder: identification of fused gene families in sequence similarity networks, Bioinformatics, vol.18, issue.7, pp.837-881, 2013.
DOI : 10.1101/gr.076588.108

URL : https://hal.archives-ouvertes.fr/hal-01544795

R. Méheust, P. Lopez, and E. Bapteste, Metabolic bacterial genes and the construction of high-level composite lineages of life, Trends in Ecology & Evolution, vol.30, issue.3, pp.127-136, 2015.
DOI : 10.1016/j.tree.2015.01.001

D. Sorokin, S. Toshchakov, T. Kolganova, and I. Kublanov, Halo(natrono)archaea isolated from hypersaline lakes utilize cellulose and chitin as growth substrates, Frontiers in Microbiology, vol.13, issue.201, p.942, 2015.
DOI : 10.1039/c1gc15193b

R. Rose, T. Brüser, J. Kissinger, and M. Pohlschröder, Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway, Molecular Microbiology, vol.6, issue.4, pp.943-50, 2002.
DOI : 10.1016/S0168-6445(00)00061-9

M. Giménez, K. Dilks, and M. Pohlschröder, Haloferax volcanii twin-arginine translocation substates include secreted soluble, C-terminally anchored and lipoproteins, Molecular Microbiology, vol.20, issue.6, pp.1597-606, 2007.
DOI : 10.1128/jb.178.2.441-446.1996

S. Storf, F. Pfeiffer, K. Dilks, Z. Chen, S. Imam et al., Mutational and Bioinformatic Analysis of Haloarchaeal Lipobox-Containing Proteins, Archaea, vol.169, issue.5, p.11, 2010.
DOI : 10.1128/jb.169.5.2187-2194.1987

URL : http://downloads.hindawi.com/journals/archaea/2010/410975.pdf

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer Res, vol.27, pp.209-229, 1967.

R. Gupta, S. Naushad, and S. Baker, Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov., INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.8, issue.4, pp.1050-69, 2015.
DOI : 10.1038/ismej.2013.165

M. Lynch and J. Conery, The Origins of Genome Complexity, Science, vol.156, issue.5649, 2003.
DOI : 10.1017/S1464793100005595

URL : http://www.cs.uoregon.edu/~conery/PDF/LynchConeryScience03.pdf

N. Kapust, S. Nelson-sathi, B. Schönfeld, E. Hazkani-covo, D. Bryant et al., Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication, Genome Biology and Evolution, vol.541, issue.7637, pp.1198-209, 2018.
DOI : 10.1038/nature21031

G. Rancati, J. Moffat, A. Typas, and N. Pavelka, Emerging and evolving concepts in gene essentiality, Nature Reviews Genetics, vol.8, issue.1, pp.34-49, 2017.
DOI : 10.1038/nrclinonc.2014.163

E. Bab-dinitz, H. Shmuely, J. Maupin-furlow, J. Eichler, and B. Shaanan, Haloferax volcanii PitA: an example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families?, Bioinformatics, vol.98, issue.14, pp.671-676, 2006.
DOI : 10.1073/pnas.141236298

URL : https://academic.oup.com/bioinformatics/article-pdf/22/6/671/838494/btk043.pdf

T. Allers, S. Barak, S. Liddell, K. Wardell, and M. Mevarech, Improved Strains and Plasmid Vectors for Conditional Overexpression of His-Tagged Proteins in Haloferax volcanii, Applied and Environmental Microbiology, vol.76, issue.6, pp.1759-69, 2010.
DOI : 10.1128/AEM.02670-09

R. Thauer, A. Kaster, H. Seedorf, W. Buckel, and R. Hedderich, Methanogenic archaea: ecologically relevant differences in energy conservation, Nature Reviews Microbiology, vol.50, issue.8, pp.579-91, 2008.
DOI : 10.1016/0378-1097(83)90105-2

A. Oren, Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes, Frontiers in Microbiology, vol.4, p.315, 2013.
DOI : 10.3389/fmicb.2013.00315

URL : http://journal.frontiersin.org/article/10.3389/fmicb.2013.00315/pdf

J. Lanyi, Salt-dependent properties of proteins from extremely halophilic bacteria, Bacteriol Rev, vol.38, pp.272-90, 1974.

J. Coker, P. Dassarma, J. Kumar, J. Müller, and S. Dassarma, Transcriptional profiling of the model Archaeon Halobacterium sp. NRC-1: responses to changes in salinity and temperature, Saline Systems, vol.3, issue.1, pp.1746-1448, 2007.
DOI : 10.1186/1746-1448-3-6

A. Kurt-k?z?ldo?an, B. Abanoz, and S. Okay, Global transcriptome analysis of Halolamina sp. to decipher the salt tolerance in extremely halophilic archaea, Gene, vol.601, pp.56-64, 2017.
DOI : 10.1016/j.gene.2016.11.042

Y. Mei, H. Liu, S. Zhang, M. Yang, C. Hu et al., Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2, PLOS ONE, vol.1858, issue.11, p.184974, 2017.
DOI : 10.1371/journal.pone.0184974.s004

R. Méheust, D. Bhattacharya, J. Pathmanathan, J. Mcinerney, P. Lopez et al., Formation of chimeric genes with essential functions at the origin of eukaryotes, BMC Biology, vol.24, issue.7, p.30, 2018.
DOI : 10.1016/j.cub.2014.01.036

S. Altschul, T. Madden, A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

URL : https://academic.oup.com/nar/article-pdf/25/17/3389/3639509/25-17-3389.pdf

A. Marchler-bauer, M. Derbyshire, N. Gonzales, S. Lu, F. Chitsaz et al., CDD: NCBI's conserved domain database, Nucleic Acids Research, vol.42, issue.D1, pp.222-228, 2014.
DOI : 10.1093/database/bar058

URL : https://academic.oup.com/nar/article-pdf/43/D1/D222/7330270/gku1221.pdf

J. Huerta-cepas, D. Szklarczyk, K. Forslund, H. Cook, D. Heller et al., eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Research, vol.43, issue.D1, pp.286-93, 2015.
DOI : 10.1126/science.1240810

M. Peabody, M. Laird, C. Vlasschaert, R. Lo, and F. Brinkman, PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures, Nucleic Acids Research, vol.39, issue.D1, pp.663-671, 2016.
DOI : 10.1093/bioinformatics/bts273

URL : https://academic.oup.com/nar/article-pdf/44/D1/D663/9483403/gkv1271.pdf

K. Katoh, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-66, 2002.
DOI : 10.1093/nar/gkf436

URL : https://academic.oup.com/nar/article-pdf/30/14/3059/9488148/gkf436.pdf

J. Söding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.315, issue.5, pp.951-60, 2005.
DOI : 10.1006/jmbi.2001.5293

S. Capella-gutiérrez, J. Silla-martínez, and T. Gabaldón, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.314, issue.4, pp.1972-1975, 2009.
DOI : 10.1006/jmbi.2001.5187

L. Nguyen, H. Schmidt, V. Haeseler, A. Minh, and B. , IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies, Molecular Biology and Evolution, vol.51, issue.1, pp.268-74, 2015.
DOI : 10.1007/s002390010105

B. Minh, M. Nguyen, and A. Von-haeseler, Ultrafast Approximation for Phylogenetic Bootstrap, Molecular Biology and Evolution, vol.14, issue.7, pp.1188-95, 2013.
DOI : 10.1093/oxfordjournals.molbev.a025811

R. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

L. Kozlowski, IPC ??? Isoelectric Point Calculator, Biology Direct, vol.40, issue.D1, p.55, 2016.
DOI : 10.1093/nar/gkr1029

R. Méheust, A. Watson, F. Lapointe, T. Papke, R. Lopez et al., Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. Data sets 1. figshare. https:// figshare.com/s/778c566b568c24d9ec83, Accessed, vol.22

R. Méheust, A. Watson, F. Lapointe, T. Papke, R. Lopez et al., Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. Data sets 2. figshare. https:// figshare.com/s/906f41485528e4a99173, Accessed, vol.22