F. Maumus and H. Quesneville, Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter, PLoS One, vol.9, issue.4, p.94101, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02636753

D. Lisch, How important are transposons for plant evolution?, Nat Rev Genet, vol.14, issue.1, pp.49-61, 2013.

C. Feschotte, Transposable elements and the evolution of regulatory networks, Nat Rev Genet, vol.9, issue.5, pp.397-405, 2008.

G. J. Faulkner, Y. Kimura, C. O. Daub, S. Wani, C. Plessy et al., The regulated retrotransposon transcriptome of mammalian cells, Nat Genet, vol.41, issue.5, pp.563-71, 2009.

N. V. Fedoroff, Presidential address. Transposable elements, epigenetics, and genome evolution, Science, vol.338, issue.6108, pp.758-67, 2012.

I. Ahmed, A. Sarazin, C. Bowler, V. Colot, and H. Quesneville, Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis, Nucleic Acids Res, vol.39, issue.16, pp.6919-6950, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02647005

M. Ong-abdullah, J. M. Ordway, N. Jiang, S. E. Ooi, S. Y. Kok et al., Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm, Nature, vol.525, issue.7570, pp.533-540, 2015.

H. Xiao, N. Jiang, E. Schaffner, E. J. Stockinger, and E. Van-der-knaap, A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit, Science, vol.319, issue.5869, pp.1527-1557, 2008.

L. Quadrana, J. Almeida, R. Asis, T. Duffy, P. G. Dominguez et al., Natural occurring epialleles determine vitamin E accumulation in tomato fruits, Nat Commun, vol.5, p.3027, 2014.

S. Zhong, Z. Fei, Y. R. Chen, Y. Zheng, M. Huang et al., Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening, Nat Biotechnol, vol.31, issue.2, pp.154-163, 2013.

J. Vrebalov, D. Ruezinsky, V. Padmanabhan, R. White, D. Medrano et al., A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus, Science, vol.296, issue.5566, pp.343-349, 2002.

, The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution, Nature, vol.485, issue.7400, pp.635-676, 2012.

M. Mehra, I. Gangwar, and R. Shankar, A deluge of complex repeats: the Solanum genome, PLoS One, vol.10, issue.8, p.133962, 2015.

J. Jakowitsch, M. F. Mette, J. Van-der-winden, M. A. Matzke, and A. J. Matzke, Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants, Proc Natl Acad Sci, vol.96, issue.23, pp.13241-13247, 1999.

A. D. Geering, F. Maumus, D. Copetti, N. Choisne, D. J. Zwickl et al., Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution, Nat Commun, vol.5, p.5269, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02631214

J. A. Bruenn, B. E. Warner, and P. Yerramsetty, Widespread mitovirus sequences in plant genomes, PeerJ, vol.3, p.876, 2015.

J. Daron, N. Glover, L. Pingault, S. Theil, V. Jamilloux et al., Organization and evolution of transposable elements along the bread wheat chromosome 3B, Genome Biol, vol.15, issue.12, p.546, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02630315

F. Maumus and H. Quesneville, Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana, Nat Commun, vol.5, p.4104, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02633174

C. Hoede, S. Arnoux, M. Moisset, T. Chaumier, O. Inizan et al., PASTEC: an automatic transposable element classification tool, PLoS One, vol.9, issue.5, p.91929, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02639360

A. Bolger, F. Scossa, M. E. Bolger, C. Lanz, F. Maumus et al., The genome of the stress-tolerant wild tomato species Solanum pennellii, Nat Genet, vol.46, issue.9, pp.1034-1042, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01204066

A. Louis, M. Muffato, R. Crollius, and H. , Genomicus: five genome browsers for comparative genomics in eukaryota, Nucleic Acids Res, vol.41, pp.700-705, 2013.

I. Makarevitch, A. J. Waters, P. T. West, M. Stitzer, C. N. Hirsch et al., Transposable elements contribute to activation of maize genes in response to abiotic stress, PLoS Genet, vol.11, issue.1, p.1004915, 2015.

T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville, Considering transposable element diversification in de novo annotation approaches, PLoS One, vol.6, issue.1, p.16526, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00568705

A. L. Price, N. C. Jones, and P. A. Pevzner, De novo identification of repeat families in large genomes, Bioinformatics, vol.21, issue.1, pp.351-359, 2005.

H. Quesneville, C. M. Bergman, O. Andrieu, D. Autard, D. Nouaud et al., Combined evidence annotation of transposable elements in genome sequences, PLoS Comput Biol, vol.1, issue.2, pp.166-75, 2005.
URL : https://hal.archives-ouvertes.fr/inserm-00000104

A. Smit, R. Hubley, P. Green, and . Repeatmasker, , 1996.

M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne et al., Circos: an information aesthetic for comparative genomics

, Genome Res, vol.19, issue.9, pp.1639-1684, 2009.

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-843, 2010.