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

C. Feschotte, N. Jiang, and S. R. Wessler, Plant transposable elements: where genetics meets genomics, Nat Rev Genet, vol.3, pp.329-341, 2002.

G. I. Arabidopsis, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, vol.408, p.796, 2000.

P. S. Schnable, D. Ware, R. S. Fulton, J. C. Stein, F. Wei et al., The B73 maize genome: complexity, diversity, and dynamics, vol.326, pp.1112-1115, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00751527

K. M. Devos, Grass genome organization and evolution, Curr Opin Plant Biol, vol.13, pp.139-145, 2010.

J. L. Bennetzen, J. Ma, and K. M. Devos, Mechanisms of recent genome size variation in flowering plants, Ann Bot, vol.95, pp.127-132, 2005.

M. I. Tenaillon, J. D. Hollister, and B. S. Gaut, A triptych of the evolution of plant transposable elements, Trends Plant Sci, vol.15, pp.471-478, 2010.

K. Naito, F. Zhang, T. Tsukiyama, H. Saito, C. N. Hancock et al., Unexpected consequences of a sudden and massive transposon amplification on rice gene expression, Nature, vol.461, pp.1130-1134, 2009.

B. Li, F. Choulet, Y. Heng, W. Hao, E. Paux et al., Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure, Plant J, vol.73, pp.952-965, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00964447

C. Vitte and J. L. Bennetzen, Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution, Proc Natl Acad Sci, vol.103, pp.17638-17643, 2006.

T. Matsumoto, J. Wu, H. Kanamori, Y. Katayose, M. Fujisawa et al., The map-based sequence of the rice genome, Nature, vol.436, pp.793-800, 2005.

A. H. Paterson, J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood et al., The Sorghum bicolor genome and the diversification of grasses, Nature, vol.457, pp.551-556, 2009.

X. Gao, Y. Hou, H. Ebina, H. L. Levin, and D. F. Voytas, Chromodomains direct integration of retrotransposons to heterochromatin, Genome Res, vol.18, pp.359-369, 2008.

I. Marín and C. Lloréns, Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data, Mol Biol Evol, vol.17, pp.1040-1049, 2000.

A. G. Chatterjee, Y. E. Leem, F. D. Kelly, and H. L. Levin, The chromodomain of Tf1 integrase promotes binding to cDNA and mediates target site selection, J Virol, vol.83, pp.2675-2685, 2009.

K. M. Devos, J. K. Brown, and J. L. Bennetzen, Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis, Genome Res, vol.12, pp.1075-1079, 2002.

J. Ma, K. M. Devos, and J. L. Bennetzen, Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice, Genome Res, vol.14, pp.860-869, 2004.

Z. Tian, C. Rizzon, J. Du, L. Zhu, J. L. Bennetzen et al., Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?, Genome Res, vol.19, pp.2221-2230, 2009.

L. Duret, G. Marais, and C. Biémont, Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans, Genetics, vol.156, pp.1661-1669, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00427072

M. Long, E. Betrán, K. Thornton, and W. Wang, The origin of new genes: glimpses from the young and old, Nat Rev Genet, vol.4, pp.865-875, 2003.

L. Yang and J. L. Bennetzen, Distribution, diversity, evolution, and survival of Helitrons in the maize genome, Proc Natl Acad Sci U S A, vol.106, pp.19922-19927, 2009.

M. Morgante, S. Brunner, G. Pea, K. Fengler, A. Zuccolo et al., Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize, Nat Genet, vol.37, pp.997-1002, 2005.

K. Hanada, V. Vallejo, K. Nobuta, R. K. Slotkin, D. Lisch et al., The functional role of pack-MULEs in rice inferred from purifying selection and expression profile, Plant Cell, vol.21, pp.25-38, 2009.

N. Jiang and S. R. Wessler, Insertion preference of maize and rice miniature inverted repeat transposable elements as revealed by the analysis of nested elements, Plant Cell, vol.13, pp.2553-2564, 2001.

N. Juretic, T. E. Bureau, and R. M. Bruskiewich, Transposable element annotation of the rice genome, Bioinformatics, vol.20, pp.155-160, 2004.

N. Jiang, C. Feschotte, X. Zhang, and S. R. Wessler, Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs), Curr Opin Plant Biol, vol.7, pp.115-119, 2004.

C. Lu, J. Chen, Y. Zhang, Q. Hu, W. Su et al., Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa, Mol Biol Evol, vol.29, pp.1005-1017, 2012.

J. Chen, Q. Hu, Y. Zhang, C. Lu, and H. Kuang, P-MITE: a database for plant miniature inverted-repeat transposable elements, Nucleic Acids Res, vol.42, pp.1176-1181, 2014.

J. L. Bennetzen, C. Coleman, R. Liu, J. Ma, and W. Ramakrishna, Consistent over-estimation of gene number in complex plant genomes, Curr Opin Plant Biol, vol.7, pp.732-736, 2004.

E. Lerat, Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs, Heredity, vol.104, pp.520-533, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00539329

F. Choulet, T. Wicker, C. Rustenholz, E. Paux, J. Salse et al., Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces, Plant Cell, vol.22, pp.1686-1701, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00964451

P. J. Sanmiguel, W. Ramakrishna, J. L. Bennetzen, C. S. Busso, and J. Dubcovsky, Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am, Funct Integr Genomics, vol.2, pp.70-80, 2002.

W. Li, P. Zhang, J. P. Fellers, B. Friebe, and B. S. Gill, Sequence composition, organization, and evolution of the core Triticeae genome, Plant J, vol.40, pp.500-511, 2004.

F. Sabot, R. Guyot, T. Wicker, N. Chantret, B. Laubin et al., Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations, Mol Genet Genomics, vol.274, pp.119-130, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00964194

E. Paux, D. Roger, E. Badaeva, G. Gay, M. Bernard et al., Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B, Plant J, vol.48, pp.463-474, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00964354

M. Charles, H. Belcram, J. Just, C. Huneau, A. Viollet et al., Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat, Genetics, vol.180, pp.1071-1086, 2008.

, TREP, the Triticeae REPeat Sequence Database

R. Brenchley, M. Spannagl, M. Pfeifer, G. L. Barker, D. 'amore et al., Analysis of the bread wheat genome using whole-genome shotgun sequencing, Nature, vol.491, pp.705-710, 2012.

H. Q. Ling, S. Zhao, D. Liu, J. Wang, H. Sun et al., Draft genome of the wheat A-genome progenitor Triticum urartu, Nature, vol.496, pp.87-90, 2013.

J. Jia, S. Zhao, X. Kong, Y. Li, G. Zhao et al., Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation, Nature, vol.496, pp.91-95, 2013.

, International Wheat Genome Sequencing Consortium

F. Choulet, A. Alberti, S. Theil, N. Glover, V. Barbe et al., Structural and functional partitioning of bread wheat chromosome 3B, Science, vol.345, p.1249721, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02638189

, IWGSC: A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome, Science, vol.345, p.1251788, 2014.

M. El-baidouri and O. Panaud, Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution
URL : https://hal.archives-ouvertes.fr/hal-01218174

, Genome Biol Evol, vol.5, pp.954-965, 2013.

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

J. P. Vogel, D. F. Garvin, T. C. Mockler, J. Schmutz, D. Rokhsar et al., Genome sequencing and analysis of the model grass Brachypodium distachyon, Nature, vol.463, pp.763-768, 2010.

R. S. Baucom, J. C. Estill, C. Chaparro, N. Upshaw, A. Jogi et al., Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome, PLoS Genet, vol.5, p.1000732, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00736178

C. Rustenholz, F. Choulet, C. Laugier, J. ?afá?, H. ?imková et al., A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat, Plant Physiol, vol.157, pp.1596-1608, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00964456

T. Wicker, R. Guyot, N. Yahiaoui, and B. Keller, CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements, Plant Physiol, vol.132, pp.52-63, 2003.

R. Liu, C. Vitte, J. Ma, A. A. Mahama, T. Dhliwayo et al., A GeneTrek analysis of the maize genome, Proc Natl Acad Sci, vol.104, pp.11844-11849, 2007.

H. Rees and M. Walters, Nuclear DNA and the evolution of wheat, Heredity, vol.20, pp.73-82, 1965.

K. Kashkush, M. Feldman, and A. A. Levy, Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat, Nat Genet, vol.33, pp.102-106, 2002.

C. Parisod, A. K. Just, J. Petit, M. Sarilar, V. Mhiri et al., Impact of transposable elements on the organization and function of allopolyploid genomes, New Phytol, vol.186, pp.37-45, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01203938

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, Y. H. Lee, Y. Jiang, X. Shi, S. Kertbundit et al., A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter, Plant Cell, vol.17, pp.1559-1568, 2005.

Y. Han, S. Qin, and S. R. Wessler, Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes, BMC Genomics, vol.14, p.71, 2013.

H. Kuang, C. Padmanabhan, F. Li, A. Kamei, P. B. Bhaskar et al., Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs, Genome Res, vol.19, pp.42-56, 2009.

, Consortium IBGS: A physical, genetic and functional sequence assembly of the barley genome, Nature, vol.491, pp.711-716, 2012.

M. A. Batzer and P. L. Deininger, Alu repeats and human genomic diversity, Nat Rev Genet, vol.3, pp.370-379, 2002.

J. S. Hawkins, H. Kim, J. D. Nason, R. A. Wing, and J. F. Wendel, Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium, Genome Res, vol.16, pp.1252-1261, 2006.

B. Piegu, R. Guyot, N. Picault, A. Roulin, A. Saniyal et al., Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice, Genome Res, vol.16, pp.1262-1269, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00164404

C. Vitte and O. Panaud, LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model, Cytogenet Genome Res, vol.110, pp.91-107, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00168793

J. S. Hawkins, S. R. Proulx, R. A. Rapp, and J. F. Wendel, Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants, Proc Natl Acad Sci U S A, vol.106, pp.17811-17816, 2009.

G. Zabala and L. O. Vodkin, The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily, Plant Cell, vol.17, pp.2619-2632, 2005.

S. Takahashi, Y. Inagaki, H. Satoh, A. Hoshino, and S. Iida, Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpn1 in the Japanese morning glory, Mol Gen Genet, vol.261, pp.447-451, 1999.

T. Wicker, J. P. Buchmann, and B. Keller, Patching gaps in plant genomes results in gene movement and erosion of colinearity, Genome Res, vol.20, pp.1229-1237, 2010.

N. Jiang, Z. Bao, X. Zhang, S. R. Eddy, and S. R. Wessler, Pack-MULE transposable elements mediate gene evolution in plants, Nature, vol.431, pp.569-573, 2004.

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.

A. J. Enright, S. Van-dongen, and C. A. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Res, vol.30, pp.1575-1584, 2002.

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res, vol.33, pp.511-518, 2005.

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, pp.1189-1191, 2009.

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

J. E. Stajich, D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz et al., The Bioperl toolkit: Perl modules for the life sciences, Genome Res, vol.12, pp.1611-1618, 2002.

J. Daron,

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

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.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximum-likelihood trees for large alignments, PLoS One, vol.5, p.9490, 2010.

R. Suzuki and H. Shimodaira, Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, vol.22, pp.1540-1542, 2006.

D. , Organization and evolution of transposable elements along the bread wheat chromosome 3B, Genome Biology, vol.15, p.546, 2014.