G. Gypsy and G. Gypsy, like like like like Hétérochromatine péricentromérique Hétérochromatine péricentromérique Hétérochromatine péricentromérique Hétérochromatine péricentromérique 16 [15-18, pp.13-15

Y. A. Abramov, G. L. Kogan, E. V. Tolchkov, V. I. Rasheva, S. A. Lavrov et al., Eu-heterochromatic Rearrangements Induce Replication of Heterochromatic Sequences Normally Underreplicated in Polytene Chromosomes of Drosophila melanogaster, Genetics, vol.171, issue.4, pp.1673-1681, 2005.
DOI : 10.1534/genetics.105.044461

M. D. Adams, R. A. Celniker, C. A. Holt, J. D. Evans, P. G. Gocayne et al., The Genome Sequence of Drosophila melanogaster, Science, vol.287, issue.5461, pp.2185-2195, 2000.
DOI : 10.1126/science.287.5461.2185

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

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 Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

E. V. Ananiev, R. L. Phillips, and H. W. Rines, Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin, Genetics, vol.149, pp.2025-2037, 1998.

E. V. Ananiev, R. L. Phillips, and H. W. Rines, Complex structure of knobs and centromeric regions in maize chromosomes, Tsitol Genet, vol.34, pp.11-15, 2000.

O. Andrieu, A. S. Fiston, D. Anxolabehere, and H. Quesneville, Detection of transposable elements by their compositional bias, BMC Bioinformatics, vol.5, issue.1, p.94, 2004.
DOI : 10.1186/1471-2105-5-94

L. Armengol, M. A. Pujana, J. Cheung, S. W. Scherer, and X. Estivill, Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements, Human Molecular Genetics, vol.12, issue.17, pp.2201-2208, 2003.
DOI : 10.1093/hmg/ddg223

M. Ashburner, Drosophila. A Laboratory Manual, 1989.
URL : https://hal.archives-ouvertes.fr/hal-00134981

J. A. Bailey, A. M. Yavor, H. F. Massa, B. J. Trask, and E. E. Eichler, Segmental Duplications: Organization and Impact Within the Current Human Genome Project Assembly, Genome Research, vol.11, issue.6, pp.1005-1017, 2001.
DOI : 10.1101/gr.GR-1871R

J. A. Bailey, Z. Gu, R. A. Clark, K. Reinert, R. V. Samonte et al., Recent Segmental Duplications in the Human Genome, Science, vol.297, issue.5583, pp.1003-1007, 2002.
DOI : 10.1126/science.1072047

J. A. Bailey and E. E. Eichler, Primate segmental duplications: crucibles of evolution, diversity and disease, Nature Reviews Genetics, vol.440, issue.7, pp.552-564, 2006.
DOI : 10.1038/nrg1895

J. L. Bennetzen and E. A. Kellogg, Do Plants Have a One-Way Ticket to Genomic Obesity?, THE PLANT CELL ONLINE, vol.9, issue.9, pp.1509-1514, 1997.
DOI : 10.1105/tpc.9.9.1509

J. L. Bennetzen, Transposable element contributions to plant gene and genome evolution, Plant Mol Biol, vol.42, pp.251-269, 2000.
DOI : 10.1007/978-94-011-4221-2_13

J. L. Bennetzen, J. Ma, and K. M. Devos, Mechanisms of Recent Genome Size Variation in Flowering Plants, Annals of Botany, vol.95, issue.1, pp.127-132, 2005.
DOI : 10.1093/aob/mci008

G. Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Research, vol.27, issue.2, pp.573-580, 1999.
DOI : 10.1093/nar/27.2.573

E. Berezikov, A. Bucheton, and I. Busseau, A search for reverse transcriptasecoding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster, Genome Biol, vol.1, p.12, 2000.

C. M. Bergman, H. Quesneville, D. Anxolabéhère, and M. Ashburner, Recurrent insertion and duplication generate networks of transposable element sequences in Drosophila melanogaster genome, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00134981

C. Biemont, C. Vieira, C. Hoogland, G. Cizeron, C. Loevenbruck et al., Maintenance of transposable element copy number in natural populations of Drosophila melanogaster and D. simulans, Genetica, vol.100, pp.161-166, 1997.
DOI : 10.1007/978-94-011-4898-6_16

URL : https://hal.archives-ouvertes.fr/hal-00434972

J. P. Blumenstiel, D. L. Hartl, and E. R. Lozovsky, Patterns of Insertion and Deletion in Contrasting Chromatin Domains, Molecular Biology and Evolution, vol.19, issue.12, pp.2211-2225, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004045

J. Brennecke, A. A. Aravin, A. Stark, M. Dus, M. Kellis et al., Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila, Cell, vol.128, issue.6, pp.1089-1103, 2007.
DOI : 10.1016/j.cell.2007.01.043

G. G. Brown, J. S. Lee, N. Brisson, and D. P. Verma, The evolution of a plant globin gene family, Journal of Molecular Evolution, vol.77, issue.1, pp.19-32, 1984.
DOI : 10.1007/BF02100624

N. Buisine, H. Quesneville, and V. Colot, Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets, Genomics, vol.91, issue.5, 2008.
DOI : 10.1016/j.ygeno.2008.01.005

URL : https://hal.archives-ouvertes.fr/hal-00280496

P. Bundock and P. Hooykaas, An Arabidopsis hAT-like transposase is essential for plant development, Nature, vol.436, issue.7048, pp.282-284, 2005.
DOI : 10.1038/nature03667

W. Burkart, T. Jung, and G. Frasch, Damage pattern as a function of radiation quality and other factors, Comptes Rendus de l'Acad??mie des Sciences - Series III - Sciences de la Vie, vol.322, issue.2-3, pp.89-101, 1999.
DOI : 10.1016/S0764-4469(99)80029-8

M. A. Carmell, A. Girard, H. J. Van-de-kant, D. Bourc-'his, T. H. Bestor et al., MIWI2 Is Essential for Spermatogenesis and Repression of Transposons in the Mouse Male Germline, Developmental Cell, vol.12, issue.4, pp.503-514, 2007.
DOI : 10.1016/j.devcel.2007.03.001

S. E. Celniker, D. A. Wheeler, B. Kronmiller, J. W. Carlson, A. Halpern et al., Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence, Genome Biol, vol.3, p.79, 2002.

B. Charlesworth, C. H. Langley, and W. Stephan, The evolution of restricted recombination and the accumulation of repeated DNA sequences, Genetics, vol.112, pp.947-962, 1986.

Z. Cheng, M. Ventura, X. She, P. Khaitovich, T. Graves et al., A genome-wide comparison of recent chimpanzee and human segmental duplications, Nature, vol.215, issue.7055, pp.88-93, 2005.
DOI : 10.1371/journal.pbio.0020207

J. Cheung, M. D. Wilson, J. Zhang, R. Khaja, J. R. Macdonald et al., Recent segmental and gene duplications in the mouse genome, Genome Biology, vol.4, issue.8, p.47, 2003.
DOI : 10.1186/gb-2003-4-8-r47

S. M. Christensen and T. H. Eickbush, R2 Target-Primed Reverse Transcription: Ordered Cleavage and Polymerization Steps by Protein Subunits Asymmetrically Bound to the Target DNA, Molecular and Cellular Biology, vol.25, issue.15, pp.6617-6628, 2005.
DOI : 10.1128/MCB.25.15.6617-6628.2005

A. G. Clark, D. R. Eisen, C. M. Smith, B. Bergman, T. A. Oliver et al., Evolution of genes and genomes on the Drosophila phylogeny, Nature, vol.2, issue.7167, pp.203-218, 2007.
DOI : 10.1038/nature06341

A. K. Csink and S. Henikoff, Something from nothing: the evolution and utility of satellite repeats, Trends in Genetics, vol.14, issue.5, pp.200-204, 1998.
DOI : 10.1016/S0168-9525(98)01444-9

M. J. Curcio and K. M. Derbyshire, The outs and ins of transposition: from mu to kangaroo, Nature Reviews Molecular Cell Biology, vol.4, issue.11, pp.865-877, 2003.
DOI : 10.1038/nrm1241

C. Dasilva, H. Hadji, C. Ozouf-costaz, S. Nicaud, O. Jaillon et al., Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome, Proceedings of the National Academy of Sciences, vol.99, issue.21, pp.13636-13641, 2002.
DOI : 10.1073/pnas.202284199

L. J. Derose-wilson and B. S. Gaut, Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata, BMC Evolutionary Biology, vol.7, issue.1, p.66, 2007.
DOI : 10.1186/1471-2148-7-66

K. M. Devos, J. K. Brown, and J. L. Bennetzen, Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis, Genome Research, vol.12, issue.7, 2002.
DOI : 10.1101/gr.132102

T. Dray and G. B. Gloor, Homology requirements for targeting heterologous sequences during P-induced gap repair in Drosophila melanogaster, Genetics, vol.147, pp.689-699, 1997.

J. Drouaud, C. Camilleri, P. Y. Bourguignon, A. Canaguier, A. Berard et al., Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots", Genome Research, vol.16, issue.1, pp.106-114, 2006.
DOI : 10.1101/gr.4319006

URL : https://hal.archives-ouvertes.fr/hal-00017439

R. C. Edgar and E. W. Myers, PILER: identification and classification of genomic repeats, Bioinformatics, vol.21, issue.Suppl 1, pp.152-158, 2005.
DOI : 10.1093/bioinformatics/bti1003

O. Elemento and O. Gascuel, An efficient and accurate distance based algorithm to reconstruct tandem duplication trees, Bioinformatics, vol.18, issue.Suppl 2, pp.92-99, 2002.
DOI : 10.1093/bioinformatics/18.suppl_2.S92

O. Elemento, O. Gascuel, and M. P. Lefranc, Reconstructing the Duplication History of Tandemly Repeated Genes, Molecular Biology and Evolution, vol.19, issue.3, pp.278-288, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004081

URL : https://hal.archives-ouvertes.fr/lirmm-00268603

H. Ellegren, Microsatellites: simple sequences with complex evolution, Nature Reviews Genetics, vol.164, issue.6, pp.435-445, 2004.
DOI : 10.1016/S0379-0738(01)00564-3

W. R. Engels, D. M. Johnson-schlitz, W. B. Eggleston, and J. Sved, High-frequency P element loss in Drosophila is homolog dependent, Cell, vol.62, issue.3, pp.515-525, 1990.
DOI : 10.1016/0092-8674(90)90016-8

D. O. Ferguson and W. K. Holloman, Recombinational repair of gaps in DNA is asymmetric in Ustilago maydis and can be explained by a migrating D-loop model., Proceedings of the National Academy of Sciences, vol.93, issue.11, pp.5419-5424, 1996.
DOI : 10.1073/pnas.93.11.5419

C. Feschotte, N. Jiang, and S. R. Wessler, PLANT TRANSPOSABLE ELEMENTS: WHERE GENETICS MEETS GENOMICS, Nature Reviews Genetics, vol.3, issue.5, pp.329-341, 2002.
DOI : 10.1038/nrg793

D. J. Finnegan, Eukaryotic transposable elements and genome evolution, Trends in Genetics, vol.5, pp.103-107, 1989.
DOI : 10.1016/0168-9525(89)90039-5

W. Fischle, Y. Wang, S. A. Jacobs, Y. Kim, C. D. Allis et al., Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains, Genes & Development, vol.17, issue.15, pp.1870-1881, 2003.
DOI : 10.1101/gad.1110503

A. S. Fiston-lavier, D. Anxolabehere, and H. Quesneville, A model of segmental duplication formation in Drosophila melanogaster, Genome Research, vol.17, issue.10, pp.1458-1470, 2007.
DOI : 10.1101/gr.6208307

W. M. Fitch, Phylogenies constrained by the crossover process as illustrated by human hemoglobins and a thirteen-cycle, eleven-amino-acid repeat in human apolipoprotein A-I, Genetics, vol.86, pp.623-644, 1977.

T. Formosa and B. M. Alberts, Purification and characterization of the T4 bacteriophage uvsX protein, J Biol Chem, vol.261, pp.6107-6118, 1986.

P. Fransz, S. Armstrong, C. Alonso-blanco, T. C. Fischer, R. A. Torres-ruiz et al., Cytogenetics for the model system Arabidopsis thaliana, The Plant Journal, vol.14, issue.6, pp.867-876, 1998.
DOI : 10.1093/nar/24.15.3017

P. F. Fransz, S. Armstrong, J. H. De-jong, L. D. Parnell, C. Van-drunen et al., Integrated Cytogenetic Map of Chromosome Arm 4S of A. thaliana, Cell, vol.100, issue.3, pp.367-376, 2000.
DOI : 10.1016/S0092-8674(00)80672-8

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

M. J. Giroux, M. Clancy, J. Baier, L. Ingham, D. Mccarty et al., De novo synthesis of an intron by the maize transposable element Dissociation., Proceedings of the National Academy of Sciences, vol.91, issue.25, pp.12150-12154, 1994.
DOI : 10.1073/pnas.91.25.12150

Y. H. Gray, It takes two transposons to tango:transposable-element-mediated chromosomal rearrangements, Trends in Genetics, vol.16, issue.10, pp.461-468, 2000.
DOI : 10.1016/S0168-9525(00)02104-1

URL : http://hdl.handle.net/1885/89003

P. Green, 2x genomes Does depth matter?, Genome Research, vol.17, issue.11, pp.1547-1549, 2007.
DOI : 10.1101/gr.7050807

URL : http://www.genome.org/cgi/content/short/17/11/1547

T. R. Gregory and P. D. Hebert, The modulation of DNA content: proximate causes and ultimate consequences, Genome Res, vol.9, pp.317-324, 1999.

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

J. E. Haber, DNA recombination: the replication connection, Trends in Biochemical Sciences, vol.24, issue.7, pp.271-275, 1999.
DOI : 10.1016/S0968-0004(99)01413-9

A. E. Hall, G. C. Kettler, and D. Preuss, Dynamic evolution at pericentromeres, Genome Research, vol.16, issue.3, pp.355-364, 2006.
DOI : 10.1101/gr.4399206

K. Harada, K. Yukuhiro, and T. Mukai, Transposition rates of movable genetic elements in Drosophila melanogaster., Proceedings of the National Academy of Sciences, vol.87, issue.8, pp.3248-3252, 1990.
DOI : 10.1073/pnas.87.8.3248

M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-174, 1985.
DOI : 10.1007/BF02101694

Y. Henry, M. Bedhomme, and G. Blanc, History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement, Trends in Plant Science, vol.11, issue.6, pp.267-273, 2006.
DOI : 10.1016/j.tplants.2006.04.002

W. G. Hill and A. Robertson, The effect of linkage on limits to artificial selection, Genetical Research, vol.18, issue.03, pp.269-294, 1966.
DOI : 10.2307/2405995

R. Holliday, The Induction of Mitotic Recombination by Mitomycin C in Ustilago and Saccharomyces, Genetics, vol.50, pp.323-335, 1964.

G. Ira and J. E. Haber, Characterization of RAD51-Independent Break-Induced Replication That Acts Preferentially with Short Homologous Sequences, Molecular and Cellular Biology, vol.22, issue.18, pp.6384-6392, 2002.
DOI : 10.1128/MCB.22.18.6384-6392.2002

A. P. Jarman and R. A. Wells, Hypervariable minisatellites: recombinators or innocent bystanders?, Trends in Genetics, vol.5, pp.367-371, 1989.
DOI : 10.1016/0168-9525(89)90171-6

Y. Ji, E. E. Eichler, S. Schwartz, and R. D. Nicholls, Structure of Chromosomal Duplicons and their Role in Mediating Human Genomic Disorders, Genome Research, vol.10, issue.5, pp.597-610, 2000.
DOI : 10.1101/gr.10.5.597

J. Jurka, Repbase Update: a database and an electronic journal of repetitive elements, Trends in Genetics, vol.16, issue.9, pp.418-420, 2000.
DOI : 10.1016/S0168-9525(00)02093-X

V. V. Kapitonov and J. Jurka, The Long Terminal Repeat of an Endogenous Retrovirus Induces Alternative Splicing and Encodes an Additional Carboxy-Terminal Sequence in the Human Leptin Receptor, Journal of Molecular Evolution, vol.48, issue.2, pp.248-251, 1999.
DOI : 10.1007/PL00013153

V. V. Kapitonov and J. Jurka, Rolling-circle transposons in eukaryotes, Proceedings of the National Academy of Sciences, vol.98, issue.15, pp.8714-8719, 2001.
DOI : 10.1073/pnas.151269298

V. V. Kapitonov and J. Jurka, Self-synthesizing DNA transposons in eukaryotes, Proceedings of the National Academy of Sciences, vol.103, issue.12, pp.4540-4545, 2006.
DOI : 10.1073/pnas.0600833103

V. V. Kapitonov and J. Jurka, Helitrons on a roll: eukaryotic rolling-circle transposons, Trends in Genetics, vol.23, issue.10, pp.521-529, 2007.
DOI : 10.1016/j.tig.2007.08.004

S. Karlin and C. Burge, Dinucleotide relative abundance extremes: a genomic signature, Trends Genet, vol.11, pp.283-290, 1995.

B. P. Kaufmann, Distribution of Induced Breaks along the X-Chromosome of Drosophila Melanogaster, Proceedings of the National Academy of Sciences, vol.25, issue.11, pp.571-577, 1939.
DOI : 10.1073/pnas.25.11.571

T. Kogoma, Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription, Microbiol Mol Biol Rev, vol.61, pp.212-238, 1997.

R. Koszul, S. Caburet, B. Dujon, and G. Fischer, Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments, The EMBO Journal, vol.23, issue.1, pp.234-243, 2004.
DOI : 10.1038/sj.emboj.7600024

R. Kunze, The Maize Transposable Element Activator (Ac), Curr Top Microbiol Immunol, vol.204, pp.161-194, 1996.
DOI : 10.1007/978-3-642-79795-8_8

M. Lachner, D. O-'carroll, S. Rea, K. Mechtler, and T. Jenuwein, Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins, Nature, vol.410, issue.6824, pp.116-120, 2001.
DOI : 10.1038/35065132

E. S. Lander, B. Linton, C. Birren, M. C. Nusbaum, J. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.6, issue.6822, pp.860-921, 2001.
DOI : 10.1038/35057062

S. E. Lee, J. K. Moore, A. Holmes, K. Umezu, R. D. Kolodner et al., Saccharomyces Ku70, Mre11/Rad50, and RPA Proteins Regulate Adaptation to G2/M Arrest after DNA Damage, Cell, vol.94, issue.3, pp.399-409, 1998.
DOI : 10.1016/S0092-8674(00)81482-8

E. Lerat, C. Biemont, and P. Capy, Codon Usage and the Origin of P Elements, Molecular Biology and Evolution, vol.17, issue.3, pp.467-468, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026326

URL : https://hal.archives-ouvertes.fr/hal-00427091

E. V. Linardopoulou, E. M. Williams, Y. Fan, C. Friedman, J. M. Young et al., Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication, Nature, vol.49, issue.7055, pp.94-100, 2005.
DOI : 10.1093/nar/gkg623

Z. Lippman, A. V. Gendrel, M. Black, M. W. Vaughn, N. Dedhia et al., Role of transposable elements in heterochromatin and epigenetic control, Nature, vol.88, issue.6998, pp.471-476, 2004.
DOI : 10.1198/1085711031256

D. P. Locke, N. Archidiacono, D. Misceo, M. F. Cardone, S. Deschamps et al., Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster, Genome Biology, vol.4, issue.8, p.50, 2003.
DOI : 10.1186/gb-2003-4-8-r50

J. R. Lydeard, S. Jain, M. Yamaguchi, and J. E. Haber, Break-induced replication and telomerase-independent telomere maintenance require Pol32, Nature, vol.408, issue.7155, pp.820-823, 2007.
DOI : 10.1016/S1097-2765(03)00269-7

X. Maside, S. Assimacopoulos, and B. Charlesworth, Rates of movement of transposable elements on the second chromosome of Drosophila melanogaster, Genetical Research, vol.75, issue.3, pp.275-284, 2000.
DOI : 10.1017/S0016672399004474

X. Maside, C. Bartolome, S. Assimacopoulos, and B. Charlesworth, Rates of movement and distribution of transposable elements in Drosophila melanogaster: in situ hybridization vs Southern blotting data, Genetics Research, vol.78, issue.02, pp.121-136, 2001.
DOI : 10.1017/S0016672301005201

R. Maxson, R. Cohn, L. Kedes, and T. Mohun, Expression and Organization of Histone Genes, Annual Review of Genetics, vol.17, issue.1, pp.239-277, 1983.
DOI : 10.1146/annurev.ge.17.120183.001323

C. B. Mc, The origin and behavior of mutable loci in maize, Proc Natl Acad Sci U S A, vol.36, pp.344-355, 1950.

B. Mcclintock, CHROMOSOME MORPHOLOGY IN ZEA MAYS, Science, vol.69, issue.1798, p.629, 1929.
DOI : 10.1126/science.69.1798.629

M. Mcvey, M. Adams, E. Staeva-vieira, and J. J. Sekelsky, Evidence for Multiple Cycles of Strand Invasion During Repair of Double-Strand Gaps in Drosophila, Genetics, vol.167, issue.2, pp.699-705, 2004.
DOI : 10.1534/genetics.103.025411

E. Montgomery, B. Charlesworth, and C. H. Langley, A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster, Genetical Research, vol.45, issue.01, pp.31-41, 1987.
DOI : 10.1007/BF00330332

D. M. Morrow, C. Connelly, and P. Hieter, Break copy" duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae, Genetics, vol.147, pp.371-382, 1997.

G. Mosig, The Essential Role of Recombination in Phage T4 Growth, Annual Review of Genetics, vol.21, issue.1, pp.347-371, 1987.
DOI : 10.1146/annurev.ge.21.120187.002023

E. W. Myers, G. G. Sutton, A. L. Delcher, I. M. Dew, D. P. Fasulo et al., A Whole-Genome Assembly of Drosophila, Science, vol.287, issue.5461, pp.2196-2204, 2000.
DOI : 10.1126/science.287.5461.2196

N. Nassif, J. Penney, S. Pal, W. R. Engels, and G. B. Gloor, Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair., Molecular and Cellular Biology, vol.14, issue.3, pp.1613-1625, 1994.
DOI : 10.1128/MCB.14.3.1613

S. B. Needleman and C. D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, pp.443-453, 1970.
DOI : 10.1016/0022-2836(70)90057-4

M. Nei and A. P. Rooney, Concerted and Birth-and-Death Evolution of Multigene Families, Annual Review of Genetics, vol.39, issue.1, pp.121-152, 2005.
DOI : 10.1146/annurev.genet.39.073003.112240

T. L. Newman, E. Tuzun, V. A. Morrison, K. E. Hayden, M. Ventura et al., A genome-wide survey of structural variation between human and chimpanzee, Genome Research, vol.15, issue.10, pp.1344-1356, 2005.
DOI : 10.1101/gr.4338005

D. I. Nurminsky, Y. Shevelyov, S. V. Nuzhdin, and V. A. Gvozdev, Structure, molecular evolution and maintenance of copy number of extended repeated structures in the X-heterochromatin of Drosophila melanogaster, Chromosoma, vol.42, issue.4, pp.277-285, 1994.
DOI : 10.1007/BF00352252

S. V. Nuzhdin and T. F. Mackay, The genomic rate of transposable element movement in Drosophila melanogaster., Molecular Biology and Evolution, vol.12, issue.1, pp.180-181, 1995.
DOI : 10.1093/oxfordjournals.molbev.a040188

S. V. Nuzhdin, E. G. Pasyukova, and T. F. Mackay, Accumulation of transposable elements in laboratory lines of Drosophila melanogaster, Genetica, vol.100, pp.167-175, 1997.
DOI : 10.1007/978-94-011-4898-6_17

S. V. Nuzhdin, Sure facts, speculations, and open questions about the evolution of transposable element copy number, Genetica, vol.107, pp.129-137, 1999.
DOI : 10.1007/978-94-011-4156-7_15

O. Donnell, K. A. , and J. D. Boeke, Mighty Piwis Defend the Germline against Genome Intruders, Cell, vol.129, issue.1, pp.37-44, 2007.
DOI : 10.1016/j.cell.2007.03.028

B. A. Ozenberger and G. S. Roeder, A unique pathway of double-strand break repair operates in tandemly repeated genes., Molecular and Cellular Biology, vol.11, issue.3, pp.1222-1231, 1991.
DOI : 10.1128/MCB.11.3.1222

F. Paques and J. E. Haber, Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae, Microbiol Mol Biol Rev, vol.63, pp.349-404, 1999.

W. J. Peacock, E. S. Dennis, M. M. Rhoades, and A. J. Pryor, Highly repeated DNA sequence limited to knob heterochromatin in maize, Proceedings of the National Academy of Sciences, vol.78, issue.7, pp.4490-4494, 1981.
DOI : 10.1073/pnas.78.7.4490

V. Pereira, Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome, Genome Biology, vol.5, issue.10, p.79, 2004.
DOI : 10.1186/gb-2004-5-10-r79

D. A. Petrov, E. R. Lozovskaya, and D. L. Hartl, High intrinsic rate of DNA loss in Drosophila, Nature, vol.384, issue.6607, pp.346-349, 1996.
DOI : 10.1038/384346a0

D. A. Petrov, Y. T. Aminetzach, J. C. Davis, D. Bensasson, and A. E. Hirsh, Size Matters: Non-LTR Retrotransposable Elements and Ectopic Recombination in Drosophila, Molecular Biology and Evolution, vol.20, issue.6, pp.880-892, 2003.
DOI : 10.1093/molbev/msg102

P. Pfeiffer, W. Goedecke, and G. Obe, Mechanisms of DNA double-strand break repair and their potential to induce chromosomal aberrations, Mutagenesis, vol.15, issue.4, pp.289-302, 2000.
DOI : 10.1093/mutage/15.4.289

C. R. Preston, J. A. Sved, and W. R. Engels, Flanking duplications and deletions associated with P-induced male recombination in Drosophila, Genetics, vol.144, pp.1623-1638, 1996.

H. Quesneville, D. Nouaud, and D. Anxolabehere, Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes, Journal of Molecular Evolution, vol.57, issue.0, pp.50-59, 2003.
DOI : 10.1007/s00239-003-0007-2

H. Quesneville, C. M. Bergman, O. Andrieu, D. Autard, D. Nouaud et al., Combined Evidence Annotation of Transposable Elements in Genome Sequences, PLoS Computational Biology, vol.16, issue.2, pp.166-175, 2005.
DOI : 1367-4803(2000)016[1040:MAPETR]2.0.CO;2

URL : https://hal.archives-ouvertes.fr/hal-00009013

H. Quesneville, N. Buisine, and V. Colot, Transposable element re-annotation of the Arabidopsis genome, 2008.

D. A. Rew, The sequencing of the rat genome, European Journal of Surgical Oncology, vol.30, issue.8, pp.905-906, 2004.
DOI : 10.1016/S0748-7983(04)00129-5

W. S. Reznikoff, A. Bhasin, D. R. Davies, I. Y. Goryshin, L. A. Mahnke et al., Tn5: A Molecular Window on Transposition, Biochemical and Biophysical Research Communications, vol.266, issue.3, pp.729-734, 1999.
DOI : 10.1006/bbrc.1999.1891

J. C. Rice, S. D. Briggs, B. Ueberheide, C. M. Barber, J. Shabanowitz et al., Histone Methyltransferases Direct Different Degrees of Methylation to Define Distinct Chromatin Domains, Molecular Cell, vol.12, issue.6, pp.1591-1598, 2003.
DOI : 10.1016/S1097-2765(03)00479-9

P. Rice, I. Longden, and A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite, Trends in Genetics, vol.16, issue.6, pp.276-277, 2000.
DOI : 10.1016/S0168-9525(00)02024-2

G. F. Richard and F. Paques, Mini- and microsatellite expansions: the recombination connection, EMBO reports, vol.88, issue.2, pp.122-126, 2000.
DOI : 10.1093/embo-reports/kvd031

C. Richardson, M. E. Moynahan, and M. Jasin, Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations, Genes & Development, vol.12, issue.24, pp.3831-3842, 1998.
DOI : 10.1101/gad.12.24.3831

G. S. Roeder and G. R. Fink, DNA rearrangements associated with a transposable element in yeast, Cell, vol.21, issue.1, pp.239-249, 1980.
DOI : 10.1016/0092-8674(80)90131-2

Y. S. Rong and K. G. Golic, The homologous chromosome is an effective template for the repair of mitotic DNA double-strand breaks in Drosophila, Genetics, vol.165, pp.1831-1842, 2003.

E. Rubin and A. A. Levy, Abortive gap repair: underlying mechanism for Ds element formation., Molecular and Cellular Biology, vol.17, issue.11, pp.6294-6302, 1997.
DOI : 10.1128/MCB.17.11.6294

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC232480

G. M. Rubin and E. B. Lewis, A Brief History of Drosophila's Contributions to Genome Research, Science, vol.287, issue.5461, pp.2216-2218, 2000.
DOI : 10.1126/science.287.5461.2216

R. V. Samonte and E. E. Eichler, OPINIONSegmental duplications and the evolution of the primate genome, Nature Reviews Genetics, vol.3, issue.1, pp.65-72, 2002.
DOI : 10.1038/nrg705

P. Sanmiguel, A. Tikhonov, Y. K. Jin, N. Motchoulskaia, D. Zakharov et al., Nested Retrotransposons in the Intergenic Regions of the Maize Genome, Science, vol.274, issue.5288, pp.765-768, 1996.
DOI : 10.1126/science.274.5288.765

P. Sanmiguel, B. S. Gaut, A. Tikhonov, Y. Nakajima, and J. L. Bennetzen, The paleontology of intergene retrotransposons of maize, Nat Genet, vol.20, pp.43-45, 1998.

X. She, Z. Jiang, R. A. Clark, G. Liu, Z. Cheng et al., Shotgun sequence assembly and recent segmental duplications within the human genome, Nature, vol.428, issue.7011, pp.927-930, 2004.
DOI : 10.1126/science.1098918

Y. Y. Shevelyov, Copies of a Stellate gene variant are located in the X heterochromatin of Drosophila melanogaster and are probably expressed, Genetics, vol.132, pp.1033-1037, 1992.

D. C. Shields and P. M. Sharp, Evidence that mutation patterns vary among Drosophila transposable elements, Journal of Molecular Biology, vol.207, issue.4, pp.843-846, 1989.
DOI : 10.1016/0022-2836(89)90252-0

K. Shirasu, A. H. Schulman, T. Lahaye, and P. Schulze-lefert, A Contiguous 66-kb Barley DNA Sequence Provides Evidence for Reversible Genome Expansion, Genome Research, vol.10, issue.7, pp.908-915, 2000.
DOI : 10.1101/gr.10.7.908

P. Stankiewicz and J. R. Lupski, Genome architecture, rearrangements and genomic disorders, Trends in Genetics, vol.18, issue.2, pp.74-82, 2002.
DOI : 10.1016/S0168-9525(02)02592-1

N. Sugawara, F. Paques, M. Colaiacovo, and J. E. Haber, Role of Saccharomyces cerevisiae Msh2 and Msh3 repair proteins in double-strand break-induced recombination, Proceedings of the National Academy of Sciences, vol.94, issue.17, pp.9214-9219, 1997.
DOI : 10.1073/pnas.94.17.9214

F. L. Sun, M. H. Cuaycong, C. A. Craig, L. L. Wallrath, J. Locke et al., The fourth chromosome of Drosophila melanogaster: Interspersed euchromatic and heterochromatic domains, Proceedings of the National Academy of Sciences, vol.97, issue.10, pp.5340-5345, 2000.
DOI : 10.1073/pnas.090530797

H. Sun, D. Treco, and J. W. Szostak, Extensive 3???-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site, Cell, vol.64, issue.6, pp.1155-1161, 1991.
DOI : 10.1016/0092-8674(91)90270-9

J. W. Szostak, T. L. Orr-weaver, R. J. Rothstein, and F. W. Stahl, The double-strand-break repair model for recombination, Cell, vol.33, issue.1, pp.25-35, 1983.
DOI : 10.1016/0092-8674(83)90331-8

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

A. V. Tulin, G. L. Kogan, D. Filipp, M. D. Balakireva, and V. A. Gvozdev, Heterochromatic Stellate gene cluster in Drosophila melanogaster: structure and molecular evolution, Genetics, vol.146, pp.253-262, 1997.

J. C. Venter, E. W. Adams, P. W. Myers, R. J. Li, G. G. Mural et al., The Sequence of the Human Genome, Science, vol.291, issue.5507, pp.1304-1351, 2001.
DOI : 10.1126/science.1058040

URL : https://hal.archives-ouvertes.fr/hal-00465088

A. E. Vinogradov, Selfish DNA is maladaptive: evidence from the plant Red List, Trends in Genetics, vol.19, issue.11, pp.609-614, 2003.
DOI : 10.1016/j.tig.2003.09.010

A. E. Vinogradov, Genome size and extinction risk in vertebrates, Proceedings of the Royal Society B: Biological Sciences, vol.271, issue.1549, pp.1701-1705, 2004.
DOI : 10.1098/rspb.2004.2776

J. B. Virgin and J. P. Bailey, The M26 hotspot of Schizosaccharomyces pombe stimulates meiotic ectopic recombination and chromosomal rearrangements, Genetics, vol.149, pp.1191-1204, 1998.

C. Vitte, O. Panaud, and H. Quesneville, LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss, BMC Genomics, vol.8, issue.1, p.218, 2007.
DOI : 10.1186/1471-2164-8-218

G. L. Waring and J. C. Pollack, Cloning and characterization of a dispersed, multicopy, X chromosome sequence in Drosophila melanogaster., Proceedings of the National Academy of Sciences, vol.84, issue.9, pp.2843-2847, 1987.
DOI : 10.1073/pnas.84.9.2843

R. H. Waterston, E. Lindblad-toh, J. Birney, J. F. Rogers, P. Abril et al., Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, pp.520-562, 2002.

J. L. Weber and E. W. Myers, Human whole-genome shotgun sequencing, Genome Res, vol.7, pp.401-409, 1997.

T. Wicker, N. Yahiaoui, R. Guyot, E. Schlagenhauf, Z. D. Liu et al., Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat, THE PLANT CELL ONLINE, vol.15, issue.5, pp.1186-1197, 2003.
DOI : 10.1105/tpc.011023

T. Wicker, F. Sabot, A. Hua-van, J. L. Bennetzen, P. Capy et al., A unified classification system for eukaryotic transposable elements, Nature Reviews Genetics, vol.8, issue.12, pp.973-982, 2007.
DOI : 10.1038/nrg2165

URL : https://hal.archives-ouvertes.fr/hal-00169819

S. I. Wright, N. Agrawal, and T. E. Bureau, Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana, Genome Res, vol.13, pp.1897-1903, 2003.

G. Yang, F. Zhang, C. N. Hancock, and S. R. Wessler, Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana, Proceedings of the National Academy of Sciences, vol.104, issue.26, pp.10962-10967, 2007.
DOI : 10.1073/pnas.0702080104

Z. Yang, PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-556, 1997.
DOI : 10.1093/bioinformatics/13.5.555

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.322.1650