C. S. Kumar, S. F. Qureshi, A. Ali, M. L. Satyanarayana, A. Rangaraju et al., Hidden magicians of genome evolution, Indian J Med Res, vol.137, issue.6, pp.1052-60, 2013.

T. Wicker, F. Sabot, A. Hua-van, J. L. Bennetzen, P. Capy et al., A unified classification system for eukaryotic transposable elements, Nat Rev Genet, vol.8, issue.12, pp.973-82, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00169819

N. Zamudio and D. Bourc'his, Transposable elements in the mammalian germline: a comfortable niche or a deadly trap ?, Heredity, vol.105, issue.1, pp.92-104, 2010.

R. Ollinger, A. J. Childs, H. M. Burgess, R. M. Speed, P. R. Lundegaard et al., Deletion of the pluripotency-associated Tex19.1 gene causes activation of endogenous retroviruses and defective spermatogenesis in mice, Plos Gen, vol.4, p.1000199, 2008.

J. Reichmann, J. P. Reddington, D. Best, D. Read, R. Ollinger et al., The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice, Hum Mol Genet, vol.22, issue.9, pp.1791-806, 2013.

Y. Tarabay, E. Kieffer, M. Teletin, C. Celebi, A. Van-montfoort et al., The mammalian-specific Tex19.1 gene plays an essential role in spermatogenesis and placenta-supported development, Hum Reprod, vol.28, issue.8, pp.2201-2215, 2013.

S. Kuntz, E. Kieffer, L. Bianchetti, N. Lamoureux, G. Furhmann et al., Tex19, a mammalian-specific protein with a restricted expression in pluripotent stem cells and germ line, Stem Cells, vol.26, issue.3, pp.734-778, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00283096

D. Tautz and T. Domazet-loso, The evolutionary origin of orphan genes, Nat Rev Genet, vol.12, issue.10, pp.692-702, 2011.

P. J. Wang, J. R. Mccarrey, F. Yang, and D. C. Page, An abundance of X-linked genes expressed in spermatogonia, Nat Genet, vol.27, issue.4, pp.422-428, 2001.

F. Prosdocimi, B. Linard, P. Pontarotti, O. Poch, and J. D. Thompson, Controversies in modern evolutionary biology: the imperative for error detection and quality control, BMC Genomics, vol.13, p.5, 2012.
URL : https://hal.archives-ouvertes.fr/inserm-00682055

C. Celebi, A. Van-montfoort, V. Skory, E. Kieffer, S. Kuntz et al., Tex 19 paralogs exhibit a gonad and placenta-specific expression in the mouse, J Reprod Dev, vol.58, issue.3, pp.360-365, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00746525

K. A. Slentz-kesler, L. P. Hale, and R. E. Kaufman, Identification and characterization of K12 (SECTM1), a novel human gene that encodes a Golgi-associated protein with transmembrane and secreted isoforms, Genomics, vol.47, issue.3, pp.327-367, 1998.

S. D. Lyman, S. Escobar, A. M. Rousseau, A. Armstrong, and W. C. Fanslow, Identification of CD7 as a cognate of the human K12 (SECTM1) protein, J Biol Chem, vol.275, issue.5, pp.3431-3438, 2000.

D. Howie, G. Rueda, H. Brown, M. H. Waldmann, and H. , Secreted and transmembrane 1A is a novel co-stimulatory ligand, Plos one, vol.8, issue.9, p.73610, 2013.
DOI : 10.1371/journal.pone.0073610
URL : https://doi.org/10.1371/journal.pone.0073610

G. K. Lam, H. X. Liao, Y. Xue, S. M. Alam, R. M. Scearce et al., Expression of the CD7 ligand K-12 in human thymic epithelial cells: regulation by IFN-gamma, J Clin Immunol, vol.25, issue.1, pp.41-50, 2005.

L. Liu, Y. Li, S. Li, N. Hu, Y. He et al., Comparison of next-generation sequencing systems, J Biomed Biotechnol, p.251364, 2012.

J. Henson, G. Tischler, and Z. Ning, Next generation sequencing and large genome assemblies, Pharmacogenomics, vol.13, issue.8, pp.901-916, 2012.
DOI : 10.2217/pgs.12.72
URL : http://europepmc.org/articles/pmc3960634?pdf=render

K. Lindblad-toh, M. Garber, O. Zuk, M. F. Lin, B. J. Parker et al., A high-resolution map of human evolutionary constraint using 29 mammals, Nature, vol.478, issue.7370, pp.476-82, 2011.

R. J. Asher, N. Bennett, and T. Lehmann, The new framework for understanding placental mammal evolution, Bioessays, vol.31, issue.8, pp.853-64, 2009.

A. C. English, S. Richards, Y. Han, M. Wang, V. Vee et al., Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology, Plos One, vol.7, issue.11, p.47768, 2012.
DOI : 10.1371/journal.pone.0047768
URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0047768&type=printable

W. C. Warren, Genome analysis of the platypus reveals unique signatures of evolution, Nature, vol.453, issue.7192, pp.175-83, 2008.

M. B. Renfree, Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development, Genome Biol, vol.12, issue.18, p.81, 2011.

O. Lecompte, J. D. Thompson, F. Plewniak, J. Thierry, and O. Poch, Multiple alignment of complete sequences (MACS) in the post-genomic era, Gene, vol.270, issue.1-2, pp.17-30, 2001.

D. Ochoa and F. Pazos, Studying the co-evolution of proteins families with the Mirrortree web server, Bioinformatics, vol.26, issue.10, pp.1370-1371, 2010.

F. Pazos and A. Valencia, Protein co-evolution, co-adaptation and interactions, EMBO J, vol.27, issue.20, pp.2648-55, 2008.
DOI : 10.1038/emboj.2008.189
URL : http://emboj.embopress.org/content/27/20/2648.full.pdf

K. J. Fryxell, The coevolution of gene family trees, Trends Genet, vol.12, issue.9, pp.364-373, 1996.

R. E. Van-kesteren, C. P. Tensen, A. B. Smit, J. Van-minnen, L. F. Kolakowski et al., Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides, J Biol Chem, vol.271, issue.7, pp.3619-3645, 1996.

M. Kawaguchi, K. Inoue, I. Luchi, M. Nishida, and S. Yasumasu, Molecular co-evolution of a protease and its substrate elucidated by analysis of the activity of predicted ancestral hatching enzyme, BMC Evol Biol, vol.13, p.231, 2013.

F. Jacob and J. Monod, Genetic regulatory mechanisms in the synthesis of proteins, J Mol Biol, vol.3, pp.318-56, 1961.

P. Michalak, Coexpression, coregulation and cofunctionality of neighboring genes in eukaryotic genomes, Genomics, vol.91, issue.3, pp.243-251, 2008.

A. Thévenin, L. Ein-dor, M. Ozery-flato, and R. Shamir, Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome, Nucleic Acids Res, vol.42, issue.15, pp.9854-61, 2014.

K. A. Brayton, C. Zhengdao, G. Zhou, P. L. Nagy, A. Gavalas et al., Two genes for de novo purine nucleotide synthesis on human chromosome 4 are closely linked and divergently transcribed, J Biol Chem, vol.269, issue.7, pp.5313-5315, 1994.

T. Blumenthal, D. Evans, C. D. Link, A. Guffanti, D. Lawson et al., A global analysis of Caenorhabditis elegans operons, Nature, vol.417, pp.851-855, 2002.

D. Brawand, M. Soumillon, A. Necsulea, P. Julien, G. Csardi et al., The evolution of gene expression levels in mammalian organs, Nature, vol.478, issue.7369, pp.343-351, 2011.

J. Merkin, C. Russell, P. Chen, and C. B. Burge, Evolutionary dynamics of gene and isoform regulation in Mammalian tissues, Science, vol.338, issue.6114, pp.1593-1602, 2012.

O. Türeci, M. Koslowski, G. Helftenbein, J. Castle, C. Rohde et al., Claudin-18 gene structure, regulation, and expression is evolutionary conserved in mammals, Gene, vol.481, issue.2, pp.83-92, 2011.

J. A. Cridland, E. Z. Curley, M. N. Wykes, K. Schroder, M. J. Sweet et al., The mammalian PYHIN gene family: phylogeny, evolution and expression, BMC Evol Biol, vol.12, p.140, 2012.
DOI : 10.1186/1471-2148-12-140
URL : https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-12-140

Y. Kodama, M. Shumway, and R. Leinonen, The Sequence Read Archive: explosive growth of sequencing data, Nucleic Acids Res, vol.40, pp.54-60, 2012.

F. Plewniak, L. Bianchetti, Y. Brelivet, A. Carles, F. Chalmel et al., PipeAlign: a new toolkit for protein family analysis, Nucleic Acids Res, vol.31, issue.13, pp.3929-832, 2003.

A. M. Waterhouse, J. B. Procter, D. M. Martin, M. Clamp, and G. J. Barton, Jalview Version 2-a multiple sequence alignment editor and analysis workbench, Bioinformatics, vol.25, issue.9, pp.1189-91, 2009.
DOI : 10.1093/bioinformatics/btp033
URL : https://academic.oup.com/bioinformatics/article-pdf/25/9/1189/526576/btp033.pdf

G. E. Crooks, G. Hon, J. M. Chandonia, and S. E. Brenner, WebLogo: a sequence logo generator, Genome Res, vol.14, issue.6, pp.1188-90, 2004.
DOI : 10.1101/gr.849004
URL : http://genome.cshlp.org/content/14/6/1188.full.pdf

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol, vol.28, issue.10, pp.2731-2740, 2011.
DOI : 10.1093/molbev/msr121
URL : https://academic.oup.com/mbe/article-pdf/28/10/2731/2954190/msr121.pdf

F. Abascal, R. Zardoya, and D. Posada, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, vol.21, issue.9, pp.2104-2109, 2005.

I. Letunic and P. Bork, Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Res, vol.39, pp.475-478, 2011.

P. Fariselli, I. Rossi, E. Capriotti, and R. Casadio, The WWWH of remote homolog detection: the state of the art, Brief Bioinform, vol.8, issue.2, pp.78-87, 2007.

J. Söding, A. Biegert, and A. N. Lupas, The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res, vol.33, pp.244-248, 2005.

C. Branden and J. Tooze, From Recognition of Foreign Molecules by the Immune System, pp.299-323, 1998.

M. Wiederstein and M. J. Sippl, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res, vol.35, pp.407-417, 2007.

I. Bosnjak, V. Bojovic, T. Segvic-bubic, and A. Bielen, Occurrence of protein disulfide bonds in different domains of life: a comparison of proteins from the Protein Data Bank, Protein Eng Des Sel, vol.27, issue.3, pp.65-72, 2014.

S. S. Krishna, I. Majumdar, and N. V. Grishin, Structural classification of zinc fingers: survey and summary, Nucleic Acids Res, vol.31, issue.2, pp.532-50, 2003.

J. Wang, Y. Yan, T. Garrett, J. Liu, D. W. Rodgers et al., Atomic structure of a fragment of human CD4 containing two immunoglobulin-like domains, Nature, vol.348, pp.411-419, 1990.

T. Wang, Y. Ge, M. Xiao, A. Lopez-coral, L. Li et al., SECTM1 produced by tumor cells attracts human monocytes via CD7-mediated activation of the PI3K pathway, J Invest Dermatol, vol.134, issue.4, pp.1108-1126, 2014.

A. Koito and T. Ikeda, Intrinsic immunity against retrotransposons by APOBEC cytidine deaminases, Front Microbiol, vol.4, p.28, 2013.

H. E. Volkman and D. B. Stetson, The enemy within: endogenous retroelements and autoimmune disease, Nat Immunol, vol.15, issue.5, pp.415-437, 2014.

A. Moffett and C. Loke, Immunology of placentation in eutherian mammals, Nat Rev Immunol, vol.6, issue.8, pp.584-94, 2006.

M. Fijak and A. Meinhardt, The testis in immune privilege, Immunol Rev, vol.213, pp.66-81, 2006.

N. D. Trinklein, S. F. Aldred, S. J. Hartman, D. I. Schroeder, R. P. Otillar et al., An abundance of bidirectional promoters in the human genome, Genome Res, vol.14, pp.62-68, 2004.

. Genome, . Community, and . Scientists, Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species, J Heredity, vol.100, issue.6, pp.659-74, 2009.