L. Cited-altschul and S. , Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

D. Alvarez-ponce, P. Lopez, E. Bapteste, and J. Mcinerney, Gene similarity networks provide tools for understanding eukaryote origins and evolution, Proceedings of the National Academy of Sciences, vol.110, issue.17, pp.1594-1603, 2013.
DOI : 10.1073/pnas.1211371110

L. Aravind and E. Koonin, Phosphoesterase domains associated with DNA polymerases of diverse origins, Nucleic Acids Research, vol.26, issue.16, pp.3746-3752, 1998.
DOI : 10.1093/nar/26.16.3746

S. Aves, Y. Liu, and T. Richards, Evolutionary Diversification of Eukaryotic DNA Replication Machinery, Subcell Biochem, vol.62, pp.19-35, 2012.
DOI : 10.1007/978-94-007-4572-8_2

B. Baker, Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis, Science, vol.314, issue.5807, pp.1933-1935, 2006.
DOI : 10.1126/science.1132690

B. Baker, Enigmatic, ultrasmall, uncultivated Archaea, Proceedings of the National Academy of Sciences, vol.107, issue.19, pp.8806-8811, 2010.
DOI : 10.1073/pnas.0914470107

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889320

E. Bapteste, C. Brochier, and Y. Boucher, Higher-level classification of the Archaea: evolution of methanogenesis and methanogens, Archaea, vol.7, issue.5, pp.353-363, 2005.
DOI : 10.1155/2005/859728

E. Barry and S. Bell, DNA Replication in the Archaea, Microbiology and Molecular Biology Reviews, vol.70, issue.4, pp.876-887, 2006.
DOI : 10.1128/MMBR.00029-06

R. Bauer, B. Graham, and M. Trakselis, Novel Interaction of the Bacterial-Like DnaG Primase with the MCM Helicase in Archaea, Journal of Molecular Biology, vol.425, issue.8, pp.1259-1273, 2013.
DOI : 10.1016/j.jmb.2013.01.025

T. Beattie and S. Bell, Molecular machines in archaeal DNA replication, Current Opinion in Chemical Biology, vol.15, issue.5, pp.614-619, 2011.
DOI : 10.1016/j.cbpa.2011.07.017

S. Bell, DNA replication: archaeal oriGINS, BMC Biology, vol.9, issue.1, p.36, 2011.
DOI : 10.1038/nsmb974

URL : http://doi.org/10.1186/1741-7007-9-36

A. Bergerat, An atypical topoisomerase II from archaea with implications for meiotic recombination, Nature, vol.386, issue.6623, pp.414-417, 1997.
DOI : 10.1038/386414a0

J. Berthon, D. Cortez, and P. Forterre, Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation, Genome Biology, vol.9, issue.4, p.71, 2008.
DOI : 10.1186/gb-2008-9-4-r71

URL : https://hal.archives-ouvertes.fr/hal-00286285

C. Brochier, P. Forterre, and S. Gribaldo, Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox, Genome Biology, vol.5, issue.3, p.17, 2004.
DOI : 10.1186/gb-2004-5-3-r17

C. Brochier, P. Forterre, and S. Gribaldo, An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences, BMC Evolutionary Biology, vol.5, issue.1, p.36, 2005.
DOI : 10.1186/1471-2148-5-36

C. Brochier-armanet, P. Forterre, and S. Gribaldo, Phylogeny and evolution of the Archaea: one hundred genomes later, Current Opinion in Microbiology, vol.14, issue.3, pp.274-281, 2011.
DOI : 10.1016/j.mib.2011.04.015

URL : https://hal.archives-ouvertes.fr/hal-00598326

T. Buckley, C. Simon, H. Shimodaira, and G. Chambers, Evaluating Hypotheses on the Origin and Evolution of the New Zealand Alpine Cicadas (Maoricicada) Using Multiple-Comparison Tests of Tree Topology, Molecular Biology and Evolution, vol.18, issue.2, pp.223-234, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003796

I. Cann, K. Komori, H. Toh, S. Kanai, and Y. Ishino, A heterodimeric DNA polymerase: Evidence that members of Euryarchaeota possess a distinct DNA polymerase, Proceedings of the National Academy of Sciences, vol.95, issue.24, pp.14250-14255, 1998.
DOI : 10.1073/pnas.95.24.14250

Y. Chen, Biochemical and Mutational Analyses of a Unique Clamp Loader Complex in the Archaeon Methanosarcina acetivorans, Journal of Biological Chemistry, vol.280, issue.51, pp.41852-41863, 2005.
DOI : 10.1074/jbc.M508684200

N. Chia, I. Cann, and G. Olsen, Evolution of DNA Replication Protein Complexes in Eukaryotes and Archaea, PLoS ONE, vol.31, issue.6, p.10866, 2010.
DOI : 10.1371/journal.pone.0010866.s005

C. Cox, P. Foster, R. Hirt, S. Harris, and T. Embley, The archaebacterial origin of eukaryotes, Proceedings of the National Academy of Sciences, vol.105, issue.51, pp.20356-20361, 2008.
DOI : 10.1073/pnas.0810647105

G. Criscuolo, A. Gribaldo, and S. , BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.210, 2010.
DOI : 10.1186/1471-2148-10-210

M. Csuros and I. Miklos, Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model, Molecular Biology and Evolution, vol.26, issue.9, pp.2087-2095, 2009.
DOI : 10.1093/molbev/msp123

L. Cubeddu and M. White, DNA Damage Detection by an Archaeal Single-stranded DNA-binding Protein, Journal of Molecular Biology, vol.353, issue.3, pp.10-10, 2005.
DOI : 10.1016/j.jmb.2005.08.050

T. Dagan and W. Martin, The tree of one percent, Genome Biology, vol.7, issue.10, p.118, 2006.
DOI : 10.1186/gb-2006-7-10-118

F. Delsuc, H. Brinkmann, and H. Philippe, Phylogenomics and the reconstruction of the tree of life, Nature Reviews Genetics, vol.3, issue.5, pp.361-375, 2005.
DOI : 10.1038/nrg1603

URL : https://hal.archives-ouvertes.fr/halsde-00193293

M. Depamphilis and S. Bell, Genome Duplication, 2010.
DOI : 10.1016/bs.ctdb.2015.10.002

E. Desmond, C. Brochier-armanet, P. Forterre, and S. Gribaldo, On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes, Research in Microbiology, vol.162, issue.1, pp.18-18, 2010.
DOI : 10.1016/j.resmic.2010.10.004

URL : https://hal.archives-ouvertes.fr/hal-00698362

R. Edgar, 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

J. Felsenstein, Confidence Limits on Phylogenies: An Approach Using the Bootstrap, Evolution, vol.39, issue.4, pp.783-791, 1985.
DOI : 10.2307/2408678

P. Forterre, Why Are There So Many Diverse Replication Machineries?, Journal of Molecular Biology, vol.425, issue.23, pp.4714-4726, 2013.
DOI : 10.1016/j.jmb.2013.09.032

URL : https://hal.archives-ouvertes.fr/hal-00932191

P. Forterre, S. Gribaldo, D. Gadelle, and M. Serre, Origin and evolution of DNA topoisomerases, Biochimie, vol.89, issue.4, pp.427-446, 2007.
DOI : 10.1016/j.biochi.2006.12.009

URL : https://hal.archives-ouvertes.fr/hal-00194416

P. Forterre and D. Gadelle, Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms, Nucleic Acids Research, vol.37, issue.3, pp.679-692, 2009.
DOI : 10.1093/nar/gkp032

URL : https://hal.archives-ouvertes.fr/hal-00529398

P. Foster, C. Cox, and T. Embley, The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.114, issue.1, pp.2197-2207, 2009.
DOI : 10.1007/s00709-005-0135-1

T. Fukui, Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes, Genome Research, vol.15, issue.3, pp.352-363, 2005.
DOI : 10.1101/gr.3003105

O. Fü-tterer, Genome sequence of Picrophilus torridus and its implications for life around pH 0, Proceedings of the National Academy of Sciences, vol.101, issue.24, pp.9091-9096, 2004.
DOI : 10.1073/pnas.0401356101

J. Gogarten, Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes., Proceedings of the National Academy of Sciences, vol.86, issue.17, pp.6661-6665, 1989.
DOI : 10.1073/pnas.86.17.6661

N. Goldman, J. Anderson, and A. Rodrigo, Likelihood-Based Tests of Topologies in Phylogenetics, Systematic Biology, vol.49, issue.4, pp.652-670, 2000.
DOI : 10.1080/106351500750049752

B. Grabowski and Z. Kelman, Archaeal DNA Replication: Eukaryal Proteins in a Bacterial Context, Annual Review of Microbiology, vol.57, issue.1, pp.487-516, 2003.
DOI : 10.1146/annurev.micro.57.030502.090709

S. Gribaldo and C. Brochier, Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol, pp.513-521, 2009.

S. Gribaldo and C. Brochier-armanet, The origin and evolution of Archaea: a state of the art, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.1, issue.1, pp.1007-1022, 2006.
DOI : 10.1016/S0168-9525(02)02744-0

URL : https://hal.archives-ouvertes.fr/hal-00697930

S. Gribaldo and P. Cammarano, The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting Machinery, Journal of Molecular Evolution, vol.47, issue.5, pp.508-516, 1998.
DOI : 10.1007/PL00006407

S. Gribaldo and H. Philippe, Ancient Phylogenetic Relationships, Theoretical Population Biology, vol.61, issue.4, pp.391-408, 2002.
DOI : 10.1006/tpbi.2002.1593

S. Guindon, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

L. Guy and T. Ettema, The archaeal ???TACK??? superphylum and the origin of eukaryotes, Trends in Microbiology, vol.19, issue.12, pp.8-8, 2011.
DOI : 10.1016/j.tim.2011.09.002

A. Hartman, The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon, PLoS ONE, vol.5, issue.3, pp.9605-9605, 2009.
DOI : 10.1371/journal.pone.0009605.s004

F. Hartung and H. Puchta, Molecular characterization of homologues of both subunits A (SPO11) and B of the archaebacterial topoisomerase 6 in plants, Gene, vol.271, issue.1, pp.81-86, 2001.
DOI : 10.1016/S0378-1119(01)00496-6

M. Hawkins, S. Malla, M. Blythe, C. Nieduszynski, and T. Allers, Accelerated growth in the absence of DNA replication origins, Nature, vol.9, issue.7477, pp.1-16, 2013.
DOI : 10.1038/nature12650

H. Higashibata, H. Kikuchi, Y. Kawarabayasi, and I. Matsui, Helicase and Nuclease Activities of Hyperthermophile Pyrococcus horikoshii Dna2 Inhibited by Substrates with RNA Segments at 5'-End, Journal of Biological Chemistry, vol.278, issue.18, pp.15983-15990, 2003.
DOI : 10.1074/jbc.M207748200

L. Hou, G. Klug, and E. Evguenieva-hackenberg, The archaeal DnaG protein needs Csl4 for binding to the exosome and enhances its interaction with adenine-rich RNAs, RNA Biology, vol.10, issue.3, pp.415-424, 2013.
DOI : 10.1016/S0076-6879(08)02220-9

H. Huber, M. Hohn, R. R. Fuchs, T. Wimmer, and V. , A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont, Nature, vol.383, issue.6884, pp.63-67, 2002.
DOI : 10.1038/417063a

C. Hurvich and C. Tsai, Regression and time series model selection in small samples, Biometrika, vol.76, issue.2, pp.297-307, 1989.
DOI : 10.1093/biomet/76.2.297

N. Iwabe, K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata, Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes., Proceedings of the National Academy of Sciences, vol.86, issue.23, pp.9355-9359, 1989.
DOI : 10.1073/pnas.86.23.9355

L. Iyer, E. Koonin, D. Leipe, and L. Aravind, Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members, Nucleic Acids Research, vol.33, issue.12, pp.3875-3896, 2005.
DOI : 10.1093/nar/gki702

G. Jobb, A. Haeseler-von, and K. Strimmer, TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics, BMC Evolutionary Biology, vol.4, issue.1, p.18, 2004.
DOI : 10.1186/1471-2148-4-18

L. Johnson, S. Eddy, and E. Portugaly, Hidden Markov model speed heuristic and iterative HMM search procedure, BMC Bioinformatics, vol.11, issue.1, p.431, 2010.
DOI : 10.1186/1471-2105-11-431

URL : http://doi.org/10.1186/1471-2105-11-431

T. Kelly, P. Simancek, and G. Brush, Identification and characterization of a single-stranded DNA-binding protein from the archaeon Methanococcus jannaschii, Proceedings of the National Academy of Sciences, vol.95, issue.25, pp.14634-14639, 1998.
DOI : 10.1073/pnas.95.25.14634

R. Kerkhoven, F. Van-enckevort, J. Boekhorst, D. Molenaar, and R. Siezen, Visualization for genomics: the Microbial Genome Viewer, Bioinformatics, vol.20, issue.11, pp.1812-1814, 2004.
DOI : 10.1093/bioinformatics/bth159

I. Kerr, Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein, The EMBO Journal, vol.22, issue.11, 2003.
DOI : 10.1093/emboj/cdg272

H. Kishino, M. Takashi, and M. Hasegawat, Maximum likelihood inference of protein phylogeny and the origin of chloroplasts, Journal of Molecular Evolution, vol.82, issue.2, pp.151-160, 1990.
DOI : 10.1007/BF02109483

H. Kishino and M. Hasegawa, Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea, Journal of Molecular Evolution, vol.46, issue.2, pp.170-179, 1989.
DOI : 10.1007/BF02100115

S. Klinge, J. Hirst, J. Maman, T. Krude, and L. Pellegrini, An iron-sulfur domain of the eukaryotic primase is essential for RNA primer synthesis, Nature Structural & Molecular Biology, vol.261, issue.9, pp.875-877, 2007.
DOI : 10.1021/bi00063a014

K. Komori and Y. Ishino, Replication Protein A in Pyrococcus furiosus Is Involved in Homologous DNA Recombination, Journal of Biological Chemistry, vol.276, issue.28, pp.25654-25660, 2001.
DOI : 10.1074/jbc.M102423200

M. Krupovic, P. Forterre, and D. Bamford, Comparative Analysis of the Mosaic Genomes of Tailed Archaeal Viruses and Proviruses Suggests Common Themes for Virion Architecture and Assembly with Tailed Viruses of Bacteria, Journal of Molecular Biology, vol.397, issue.1, pp.17-17, 2010.
DOI : 10.1016/j.jmb.2010.01.037

URL : https://hal.archives-ouvertes.fr/hal-00506375

M. Krupovic, S. Gribaldo, D. Bamford, and P. Forterre, The Evolutionary History of Archaeal MCM Helicases: A Case Study of Vertical Evolution Combined with Hitchhiking of Mobile Genetic Elements, Molecular Biology and Evolution, vol.27, issue.12, pp.2716-2732, 2010.
DOI : 10.1093/molbev/msq161

URL : https://hal.archives-ouvertes.fr/hal-00555513

N. Lartillot, T. Lepage, and S. Blanquart, PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Bioinformatics, vol.25, issue.17, pp.2286-2288, 2009.
DOI : 10.1093/bioinformatics/btp368

E. Lasek-nesselquist and J. Gogarten, The effects of model choice and mitigating bias on the ribosomal tree of life, Molecular Phylogenetics and Evolution, vol.69, issue.1, pp.17-38, 2013.
DOI : 10.1016/j.ympev.2013.05.006

K. Makarova and E. Koonin, Archaeology of Eukaryotic DNA Replication, Cold Spring Harbor Perspectives in Biology, vol.5, issue.11, p.12963, 2013.
DOI : 10.1101/cshperspect.a012963

K. Makarova, E. Koonin, and Z. Kelman, The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes, Biology Direct, vol.7, issue.1, p.7, 2012.
DOI : 10.1038/nrmicro2406

K. Makarova, A. Sorokin, P. Novichkov, Y. Wolf, and E. Koonin, Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea, Biology Direct, vol.2, issue.1, p.33, 2007.
DOI : 10.1186/1745-6150-2-33

S. Malik, M. Ramesh, A. Hulstrand, and J. Logsdon, Protist Homologs of the Meiotic Spo11 Gene and Topoisomerase VI reveal an Evolutionary History of Gene Duplication and Lineage-Specific Loss, Molecular Biology and Evolution, vol.24, issue.12, pp.2827-2841, 2007.
DOI : 10.1093/molbev/msm217

I. Martin and S. Macneill, ATP-dependent DNA ligases, Genome Biol, vol.3, p.3005, 2002.

E. Martini and S. Keeney, Sex and the Single (Double-Strand) Break, Molecular Cell, vol.9, issue.4, pp.700-702, 2002.
DOI : 10.1016/S1097-2765(02)00512-9

O. Matte-tailliez, C. Brochier, P. Forterre, and P. H. , Archaeal Phylogeny Based on Ribosomal Proteins, Molecular Biology and Evolution, vol.19, issue.5, pp.631-639, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004122

URL : https://hal.archives-ouvertes.fr/hal-00698045

A. Mcgeoch and S. Bell, Extra-chromosomal elements and the evolution of cellular DNA replication machineries, Nature Reviews Molecular Cell Biology, vol.97, issue.7, pp.569-574, 2008.
DOI : 10.1038/nrm2426

M. Meselson and F. Stahl, The replication of DNA in Escherichia coli, Proceedings of the National Academy of Sciences, vol.44, issue.7, pp.671-682, 1958.
DOI : 10.1073/pnas.44.7.671

P. Narasingarao, De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities, The ISME Journal, vol.58, issue.1, pp.81-93, 2012.
DOI : 10.1186/gb-2008-9-10-r151

URL : https://hal.archives-ouvertes.fr/hal-00965716

E. Pagaling, Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China, BMC Genomics, vol.8, issue.1, p.410, 2006.
DOI : 10.1186/1471-2164-8-410

M. Pan, Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability, Extremophiles, vol.62, issue.3, pp.453-461, 2013.
DOI : 10.1007/s00792-013-0526-8

M. Pan, T. Santangelo, Z. Li, J. Reeve, and Z. Kelman, Thermococcus kodakarensis encodes three MCM homologs but only one is essential, Nucleic Acids Research, vol.39, issue.22, pp.9671-9680, 2011.
DOI : 10.1093/nar/gkr624

URL : http://doi.org/10.1093/nar/gkr624

S. Paytubi, Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales, Proceedings of the National Academy of Sciences, vol.109, issue.7, pp.398-405, 2012.
DOI : 10.1073/pnas.1113277108

H. Philippe, MUST, a computer package of Management Utilities for Sequences and Trees, Nucleic Acids Research, vol.21, issue.22, pp.5264-5272, 1993.
DOI : 10.1093/nar/21.22.5264

M. Podar, Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park, Biology Direct, vol.67, issue.4, p.9, 2012.
DOI : 10.1111/j.1365-2958.2007.06047.x

M. Prokofeva, Isolation of the anaerobic thermoacidophilic crenarchaeote Acidilobus saccharovorans sp. nov. and proposal of Acidilobales ord. nov., including Acidilobaceae fam. nov. and Caldisphaeraceae fam. nov., INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.59, issue.12, pp.3116-3122, 2009.
DOI : 10.1099/ijs.0.010355-0

D. Richard, Single-stranded DNA-binding protein hSSB1 is critical for genomic stability, Nature, vol.26, issue.7195, pp.677-681, 2008.
DOI : 10.1038/nature06883

C. Rinke, Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.45, issue.7459, pp.431-437, 2013.
DOI : 10.1093/bib/bbs031

J. Robbins, The Euryarchaeota, Nature's Medium for Engineering of Single-stranded DNA-binding Proteins, Journal of Biological Chemistry, vol.280, issue.15, pp.15325-15339, 2005.
DOI : 10.1074/jbc.M412870200

J. Robbins, Functional Analysis of Multiple Single-stranded DNA-binding Proteins from Methanosarcina acetivorans and Their Effects on DNA Synthesis by DNA Polymerase BI, Journal of Biological Chemistry, vol.279, issue.8, pp.6315-6326, 2004.
DOI : 10.1074/jbc.M304491200

N. Robinson and S. Bell, Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes, Proceedings of the National Academy of Sciences, vol.104, issue.14, pp.5806-5811, 2007.
DOI : 10.1073/pnas.0700206104

F. Ronquist, MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, vol.61, issue.3, pp.539-542, 2012.
DOI : 10.1093/sysbio/sys029

R. Samson, Specificity and Function of Archaeal DNA Replication Initiator Proteins, Cell Reports, vol.3, issue.2, pp.485-496, 2013.
DOI : 10.1016/j.celrep.2013.01.002

W. Shi, Essential Developmental, Genomic Stability, and Tumour Suppressor Functions of the Mouse Orthologue of hSSB1/NABP2, PLoS Genetics, vol.106, issue.2, pp.1003298-1003298, 2012.
DOI : 10.1371/journal.pgen.1003298.s014

H. Shimodaira, An Approximately Unbiased Test of Phylogenetic Tree Selection, Systematic Biology, vol.51, issue.3, pp.492-508, 2002.
DOI : 10.1080/10635150290069913

H. Shimodaira and M. Hasegawa, Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference, Molecular Biology and Evolution, vol.16, issue.8, pp.1114-1116, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026201

A. Skowyra and S. Macneill, Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism, Nucleic Acids Research, vol.40, issue.3, pp.1077-1090, 2012.
DOI : 10.1093/nar/gkr838

N. Soler, Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins, Nucleic Acids Research, vol.38, issue.15, pp.5088-5104, 2010.
DOI : 10.1093/nar/gkq236

B. Stillman, DNA Polymerases at the Replication Fork in??Eukaryotes, Molecular Cell, vol.30, issue.3, pp.259-260, 2008.
DOI : 10.1016/j.molcel.2008.04.011

A. Stroud, S. Liddell, and T. Allers, Genetic and Biochemical Identification of a Novel Single-Stranded DNA-Binding Complex in Haloferax volcanii, Frontiers in Microbiology, vol.3, pp.224-224, 2012.
DOI : 10.3389/fmicb.2012.00224

D. Szklarczyk, The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored, Nucleic Acids Research, vol.39, issue.Database, pp.561-568, 2011.
DOI : 10.1093/nar/gkq973

D. Vallenet, MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2005.
DOI : 10.1093/nar/gkj406

R. Wadsworth and M. White, Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus, Nucleic Acids Research, vol.29, issue.4, pp.914-920, 2001.
DOI : 10.1093/nar/29.4.914

A. Wilkinson, J. Day, and R. Bowater, Bacterial DNA ligases, Molecular Microbiology, vol.19, issue.6, pp.1241-1248, 2001.
DOI : 10.1046/j.1365-313x.2000.00856.x

T. Williams, P. Foster, T. Nye, C. Cox, and T. Embley, A congruent phylogenomic signal places eukaryotes within the Archaea, Proceedings of the Royal Society B: Biological Sciences, vol.25, issue.17, pp.4870-4879, 2012.
DOI : 10.1093/bioinformatics/btp368

Y. Wolf, K. Makarova, N. Yutin, and E. Koonin, Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer, Biology Direct, vol.7, issue.1, pp.46-46, 2011.
DOI : 10.1186/1745-6150-7-46

K. Yamashiro, S. Yokobori, T. Oshima, and A. Yamagishi, Structural analysis of the plasmid pTA1 isolated from the thermoacidophilic archaeon Thermoplasma acidophilum, Extremophiles, vol.128, issue.4, pp.327-335, 2006.
DOI : 10.1007/s00792-005-0502-z

N. Yutin, P. Puigbò, E. Koonin, and Y. Wolf, Phylogenomics of Prokaryotic Ribosomal Proteins, PLoS ONE, vol.193, issue.12, p.36972, 2012.
DOI : 10.1371/journal.pone.0036972.s013

R. Zhang and C. Zhang, Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii, Extremophiles, vol.8, issue.3, pp.253-258, 2004.
DOI : 10.1007/s00792-004-0385-4

A. Zhao, F. Gray, and S. Macneill, ATP- and NAD+-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii, Molecular Microbiology, vol.1749, issue.3, pp.743-752, 2006.
DOI : 10.1046/j.1365-2958.2001.02479.x