J. Bennetzen and H. Wang, The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes, Annual Review of Plant Biology, vol.65, issue.1, pp.505-535, 2014.
DOI : 10.1146/annurev-arplant-050213-035811

E. Kejnovsky and M. Lexa, Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators, Mobile Genetic Elements, vol.4, issue.1, p.28084, 2014.
DOI : 10.1128/JVI.79.19.12507-12514.2005

P. Siguier, E. Gourbeyre, and M. Chandler, Bacterial insertion sequences: their genomic impact and diversity, FEMS Microbiology Reviews, vol.38, issue.5, pp.1574-6976, 2014.
DOI : 10.1111/1574-6976.12067
URL : https://hal.archives-ouvertes.fr/hal-01117881

J. Jurka, V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany et al., Repbase Update, a database of eukaryotic repetitive elements, Cytogenetic and Genome Research, vol.110, issue.1-4, pp.462-469, 2005.
DOI : 10.1159/000084979

P. Siguier, A. Varani, J. Perochon, and M. Chandler, Exploring Bacterial Insertion Sequences with ISfinder: Objectives, Uses, and Future Developments, Methods Mol Biol, vol.859, pp.91-103, 2012.
DOI : 10.1007/978-1-61779-603-6_5
URL : https://hal.archives-ouvertes.fr/hal-00789655

S. Tempel, . Using, and . Understanding-repeatmasker, Using and Understanding RepeatMasker, Methods Mol Biol, vol.859, pp.29-51, 2012.
DOI : 10.1007/978-1-61779-603-6_2

J. Jurka, P. Klonowski, V. Dagman, and P. Pelton, Censor???a program for identification and elimination of repetitive elements from DNA sequences, Computers & Chemistry, vol.20, issue.1, pp.119-141, 1996.
DOI : 10.1016/S0097-8485(96)80013-1

T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville, Considering Transposable Element Diversification in De Novo Annotation Approaches, PLoS ONE, vol.25, issue.3, p.16526, 2011.
DOI : 10.1371/journal.pone.0016526.s021
URL : https://hal.archives-ouvertes.fr/hal-00568705

D. Karolchik, G. Barber, J. Casper, H. Clawson, M. Cline et al., The UCSC Genome Browser database: 2014 update, Nucleic Acids Research, vol.42, issue.D1, pp.764-70, 2014.
DOI : 10.1093/nar/gkt1168

P. Flicek, M. Amode, D. Barrell, K. Beal, S. Brent et al., Ensembl 2012, Nucleic Acids Research, vol.40, issue.D1, pp.84-90, 2012.
DOI : 10.1093/nar/gkr991

T. Wheeler, J. Clements, S. Eddy, R. Hubley, T. Jones et al., Dfam: a database of repetitive DNA based on profile hidden Markov models, Nucleic Acids Research, vol.41, issue.D1, pp.70-82, 2013.
DOI : 10.1093/nar/gks1265

S. Tempel, M. Jurka, and J. Jurka, VisualRepbase: an interface for the study of occurrences of transposable element families, BMC Bioinformatics, vol.9, issue.1, p.345, 2008.
DOI : 10.1186/1471-2105-9-345

M. Johnson, I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. Mcginnis et al., NCBI BLAST: a better web interface, Nucleic Acids Research, vol.36, issue.Web Server, pp.5-9, 2008.
DOI : 10.1093/nar/gkn201

O. Kohany, A. Gentles, L. Hankus, and J. Jurka, Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor, BMC Bioinformatics, vol.7, issue.1, p.474, 2006.
DOI : 10.1186/1471-2105-7-474

. The-arabidopsis-genome-initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, vol.408, issue.6814, pp.796-815, 2000.
DOI : 10.1038/35048692

V. Kapitonov and J. Jurka, Molecular paleontology of transposable elements from Arabidopsis thaliana, Genetica, vol.107, pp.27-37, 1999.
DOI : 10.1007/978-94-011-4156-7_4

V. Kapitonov and J. Jurka, Rolling-circle transposons in eukaryotes, Proceedings of the National Academy of Sciences, vol.98, issue.15, pp.8923-8927, 2001.
DOI : 10.1073/pnas.151269298

H. Kazazian, Mobile Elements: Drivers of Genome Evolution, Science, vol.303, issue.5664, pp.1626-1658, 2004.
DOI : 10.1126/science.1089670

S. Wessler, Transposable elements and the evolution of eukaryotic genomes, Proceedings of the National Academy of Sciences, vol.103, issue.47, pp.17600-17601, 2006.
DOI : 10.1073/pnas.0607612103

A. Kawabe, B. Hansson, J. Hagenblad, A. Forrest, and D. Charlesworth, Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana, Genetics, vol.173, issue.3, pp.1613-1622, 2006.
DOI : 10.1534/genetics.106.057182

M. Lyon, The Lyon and the LINE hypothesis, Seminars in Cell & Developmental Biology, vol.14, issue.6, pp.313-321, 2003.
DOI : 10.1016/j.semcdb.2003.09.015

R. Cordaux and M. Batzer, The impact of retrotransposons on human genome evolution, Nature Reviews Genetics, vol.616, issue.10, pp.691-703, 2009.
DOI : 10.1038/nrg2640
URL : https://hal.archives-ouvertes.fr/hal-00419189

A. Cultrone, Y. Domínguez, C. Drevet, C. Scazzocchio, and R. Fernández-martín, The tightly regulated promoter of the xanA gene of Aspergillus nidulans is included in a helitron, Molecular Microbiology, vol.11, issue.6, pp.1577-87, 2007.
DOI : 10.1111/j.1365-2958.2007.05609.x
URL : https://hal.archives-ouvertes.fr/hal-00195329

G. Kogan, L. Usakin, S. Ryazansky, and V. Gvozdev, Expansion and Evolution of the X-Linked Testis Specific Multigene Families in the melanogaster Species Subgroup, PLoS ONE, vol.28, issue.128, p.37738, 2012.
DOI : 10.1371/journal.pone.0037738.s005