, European Regional Development Fund (ERDF

, Funding for open access charge

G. D. Hurst and M. Schilthuizen, Selfish genetic elements and speciation, Heredity, vol.80, pp.2-8, 1998.

J. N. Volff and J. Brosius, Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes, Genome Dyn, vol.3, pp.175-190, 2007.

C. M. Fauquet, M. A. Mayo, U. Desselberger, and L. A. Ball, Virus Taxonomy, VIIIth Report of the ICTV, 2005.

J. Jurka, V. V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany et al., Repbase Update, a database of eukaryotic repetitive elements, Cytogenet. Genome Res, vol.110, pp.462-467, 2005.

R. Leplae, A. Hebrant, S. J. Wodak, and A. Toussaint, ACLAME: a CLAssification of Mobile genetic Elements, Nucleic Acids Res, vol.32, pp.45-49, 2004.

C. Llorens, R. Futami, D. Bezemer, and A. Moya, The Gypsy Database (GyDB) of mobile genetic elements, Nucleic Acids Res, vol.36, pp.38-46, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02648997

C. Llorens, A. Munoz-pomer, L. Bernad, H. Botella, and A. Moya, Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees, Biol. Direct, vol.4, p.41, 2009.

D. A. Benson, I. Karsch-mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers, GenBank. Nucleic Acids Res, vol.37, pp.26-31, 2009.

C. Llorens, M. A. Fares, and A. Moya, Relationships of Gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis, BMC Evol. Biol, vol.8, p.276, 2008.

S. R. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, pp.755-763, 1998.

E. V. Koonin, S. Zhou, and J. C. Lucchesi, The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin, Nucleic Acids Res, vol.23, pp.4229-4233, 1995.

N. D. Rawlings, A. J. Barrett, and A. Bateman, MEROPS: the peptidase database, Nucleic Acids Res, vol.38, pp.227-233, 2010.

C. Llorens, R. Futami, G. Renaud, and A. Moya, Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases, Biol. Direct, vol.4, p.3, 2009.

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402, 1997.

C. Llorens, R. Futami, M. Vicente-ripolles, and A. Moya, Phylograph: a multifunction Java editor for handling phylogenetic trees, Biotechvana Bioinformatics, 2008.

C. Llorens, A. Mun?oz-pomer, R. Futami, and A. Moya, The GyDB Collection of Viral and Mobile Genetic Element Models, Biotechvana Bioinformatics, 2009.

O. Piskurek, H. Nishihara, N. Okada, O. Novikova, V. Mayorov et al., The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis, Plant J, vol.441, pp.562-574, 2008.

Y. A. Bae, J. S. Ahn, S. H. Kim, M. G. Rhyu, Y. Kong et al., PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy, BMC. Genomics, vol.9, p.482, 2008.

D. Gao, N. Gill, H. R. Kim, J. G. Walling, W. Zhang et al., A lineage-specific centromere retrotransposon in Oryza brachyantha, Plant J, vol.60, pp.820-831, 2009.

A. M. Gottlieb and L. Poggio, Genomic screening in dioecious ''yerba mate'' tree (Ilex paraguariensis A. St. Hill., Aquifoliaceae) through representational difference analysis, Genetica, vol.138, pp.567-578, 2010.

F. Maumus, A. E. Allen, C. Mhiri, H. Hu, K. Jabbari et al., Potential impact of stress activated retrotransposons on genome evolution in a marine diatom, BMC Genomics, vol.10, p.624, 2009.

, Genome sequence of the pea aphid Acyrthosiphon pisum, The International Aphid Genomics Consortium, vol.8, p.1000313, 2010.

H. S. Malik and T. H. Eickbush, Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons, J. Virol, vol.73, pp.5186-5190, 1999.

E. Lerat, F. Brunet, C. Bazin, and P. Capy, Is the evolution of transposable elements modular?, Genetica, vol.107, pp.15-25, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00428431

T. J. Goodwin and R. T. Poulter, A group of deuterostome Ty3/ gypsy-like retrotransposons with Ty1/ copia-like pol-domain orders, Mol. Genet. Genomics, vol.267, pp.481-491, 2002.

T. H. Eickbush and H. S. Malik, Origin and evolution of retrotransposons, Mobile DNA II, pp.1111-1144, 2002.

H. S. Malik and T. H. Eickbush, Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses, Genome Res, vol.11, pp.1187-1197, 2001.

A. Marco and I. Marin, How Athila retrotransposons survive in the Arabidopsis genome, BMC. Genomics, vol.9, p.219, 2008.

A. Rambaut, D. Posada, K. A. Crandall, and E. C. Holmes, The causes and consequences of HIV evolution, Nat. Rev. Genet, vol.5, pp.52-61, 2004.

A. J. Flavell, Long terminal repeat retrotransposons jump between species, Proc. Natl Acad. Sci. USA, vol.96, pp.12211-12212, 1999.

I. K. Jordan, L. V. Matyunina, and J. F. Mcdonald, Evidence for the recent horizontal transfer of long terminal repeat retrotransposon, Proc. Natl Acad. Sci. USA, vol.96, pp.12621-12625, 1999.

M. Bousalem, E. J. Douzery, and S. E. Seal, Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences, Arch. Virol, vol.153, pp.1085-1102, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00469426

E. V. Koonin, A. R. Mushegian, E. V. Ryabov, and V. V. Dolja, Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity, J. Gen. Virol, vol.72, pp.2895-2903, 1991.

J. V. Llorens, J. B. Clark, I. Martinez-garay, S. Soriano, R. Defrutos et al., Gypsy endogenous retrovirus maintains potential infectivity in several species of Drosophilids, BMC Evol. Biol, vol.8, p.302, 2008.

N. De-setta, M. A. Van-sluys, P. Capy, and C. M. Carareto, Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila, BMC Evol. Biol, vol.9, p.279, 2009.