/. Génoscope, F. Cea, F. Government, and . Genomique, Investissements d'Avenir' programmes OCEANOMICS (ANR-11-BTBR-0008)ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), the ANR projects FRANCE GÉNOMIQUE (ANR-10-INBS-09-08, PROMETHEUS (ANR-09-GENM-031)

S. Altschul, W. Gish, W. Miller, E. Myers, and D. 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. Altschul, T. Madden, 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

D. Antoine, A. Morel, and A. J. , Algal pigment distribution and primary production in the eastern Mediterranean as derived from coastal zone color scanner observations, Journal of Geophysical Research, vol.7, issue.C8, pp.16193-16209, 1995.
DOI : 10.1029/95JC00466

D. Arambula, W. Wong, B. Medhekar, H. Guo, M. Gingery et al., Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement, Proceedings of the National Academy of Sciences, vol.110, issue.20, pp.8212-8217, 2013.
DOI : 10.1073/pnas.1301366110

I. Arkhipova, K. Pyatkov, M. Meselson, and M. Evgen-'ev, Retroelements containing introns in diverse invertebrate taxa, Nature Genetics, vol.33, issue.2, pp.123-124, 2003.
DOI : 10.1038/ng1074

E. Armbrust, J. Berges, C. Bowler, B. Green, D. Martinez et al., The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism, Science, vol.306, issue.5693, pp.79-86, 2004.
DOI : 10.1126/science.1101156

C. Arnosti, B. Fuchs, R. Amann, and U. Passow, Contrasting extracellular enzyme activities of particle-associated bacteria from distinct provinces of the North Atlantic Ocean, Frontiers in Microbiology, vol.3, p.425, 2012.
DOI : 10.3389/fmicb.2012.00425

R. Aziz, M. Breitbart, and R. Edwards, Transposases are the most abundant, most ubiquitous genes in nature, Nucleic Acids Research, vol.38, issue.13, pp.4207-4217, 2010.
DOI : 10.1093/nar/gkq140

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.505-530, 2014.
DOI : 10.1146/annurev-arplant-050213-035811

B. Berland, D. Bonin, and S. Maestrini, Azote ou phosphore? Considerations sur le 'paradoxe nutrionnel' de la mer Mediterranee, Oceanol Acta, vol.3, pp.135-142, 1980.

G. Blanc, G. Duncan, I. Agarkova, M. Borodovsky, J. Gurnon et al., NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex, The Plant Cell, vol.22, issue.9, pp.2943-2955, 2010.
DOI : 10.1105/tpc.110.076406

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965543

G. Blanc, I. Agarkova, J. Grimwood, A. Kuo, A. Brueggeman et al., The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation, Genome Biology, vol.13, issue.5, p.39, 2012.
DOI : 10.1080/10635150600755453

P. Bork, C. Bowler, C. De-vargas, G. Gorsky, E. Karsenti et al., Tara Oceans studies plankton at planetary scale, Science, vol.348, issue.6237, p.873, 2015.
DOI : 10.1126/science.aac5605

URL : https://hal.archives-ouvertes.fr/hal-01258211

C. Bowler, A. Allen, J. Badger, J. Grimwood, K. Jabbari et al., The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, vol.9, issue.7219, pp.239-244, 2008.
DOI : 10.1038/nature07410

URL : https://hal.archives-ouvertes.fr/cea-00910244

F. Bringaud, M. Muller, G. Cerqueira, M. Smith, R. A. Sayed et al., Members of a Large Retroposon Family Are Determinants of Post-Transcriptional Gene Expression in Leishmania, PLoS Pathogens, vol.11, issue.9, pp.1291-1307, 2007.
DOI : 10.1371/journal.ppat.0030136.st003

S. Bulman, J. Candy, M. Fiers, R. Lister, A. Conner et al., Genomics of Biotrophic, Plant-infecting Plasmodiophorids Using In Vitro Dual Cultures, Protist, vol.162, issue.3, pp.449-461, 2011.
DOI : 10.1016/j.protis.2010.09.004

M. Carr, M. Nelson, B. Leadbeater, and S. Baldauf, Three Families of LTR Retrotransposons are Present in the Genome of the Choanoflagellate Monosiga brevicollis, Protist, vol.159, issue.4, pp.579-590, 2008.
DOI : 10.1016/j.protis.2008.05.001

E. Casacuberta and J. Gonzalez, The impact of transposable elements in environmental adaptation, Molecular Ecology, vol.100, issue.38, pp.1503-1517, 2013.
DOI : 10.1111/mec.12170

F. Choulet, A. Alberti, S. Theil, N. Glover, V. Barbe et al., Structural and functional partitioning of bread wheat chromosome 3B, Science, vol.345, issue.6194, p.1249721, 2014.
DOI : 10.1126/science.1249721

J. Collen, B. Porcel, W. Carre, S. Ball, C. Chaparro et al., Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida, Proceedings of the National Academy of Sciences, vol.110, issue.13, pp.5247-5252, 2013.
DOI : 10.1073/pnas.1221259110

URL : https://hal.archives-ouvertes.fr/hal-01073830

D. Ortenzio, F. Ribera-d-'alcala, and M. , On the trophic regimes of the Mediterranean Sea: a satellite analysis, Biogeosciences, vol.6, issue.2, pp.139-148, 2009.
DOI : 10.5194/bg-6-139-2009

C. De-vargas, S. Audic, N. Henry, J. Decelle, F. Mahe et al., Eukaryotic plankton diversity in the sunlit ocean, Science, vol.348, issue.6237, p.1261605, 2015.
DOI : 10.1126/science.1261605

A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet et al., Phylogeny.fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Research, vol.36, issue.Web Server, pp.465-469, 2008.
DOI : 10.1093/nar/gkn180

URL : https://hal.archives-ouvertes.fr/lirmm-00324099

E. Derelle, C. Ferraz, S. Rombauts, P. Rouze, A. Worden et al., Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features, Proceedings of the National Academy of Sciences, vol.103, issue.31, pp.11647-11652, 2006.
DOI : 10.1073/pnas.0604795103

URL : https://hal.archives-ouvertes.fr/hal-00164247

W. Doolittle and C. Sapienza, Selfish genes, the phenotype paradigm and genome evolution, Nature, vol.284, issue.5757, pp.601-603, 1980.
DOI : 10.1038/284601a0

M. Dreyfus and P. Regnier, The Poly(A) Tail of mRNAs, Cell, vol.111, issue.5, pp.611-613, 2002.
DOI : 10.1016/S0092-8674(02)01137-6

K. Dunlap, M. Palmarini, M. Varela, R. Burghardt, K. Hayashi et al., Endogenous retroviruses regulate periimplantation placental growth and differentiation, Proceedings of the National Academy of Sciences, vol.103, issue.39, pp.14390-14395, 2006.
DOI : 10.1073/pnas.0603836103

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1599973

R. Finn, J. Clements, and S. Eddy, HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.39, issue.suppl, pp.29-37, 2011.
DOI : 10.1093/nar/gkr367

URL : http://doi.org/10.1093/nar/gkr367

M. Frada, D. Schatz, V. Farstey, J. Ossolinski, H. Sabanay et al., Zooplankton May Serve as Transmission Vectors for Viruses Infecting Algal Blooms in the Ocean, Current Biology, vol.24, issue.21, pp.2592-2597, 2014.
DOI : 10.1016/j.cub.2014.09.031

J. Galagan, S. Calvo, K. Borkovich, E. Selker, N. Read et al., The genome sequence of the filamentous fungus Neurospora crassa, Nature, vol.422, issue.6934, pp.859-868, 2003.
DOI : 10.1038/nature01554

W. Gifford, S. Pfaff, and T. Macfarlan, Transposable elements as genetic regulatory substrates in early development, Trends in Cell Biology, vol.23, issue.5, pp.218-226, 2013.
DOI : 10.1016/j.tcb.2013.01.001

E. Gladyshev and I. Arkhipova, A widespread class of reverse transcriptase-related cellular genes, Proceedings of the National Academy of Sciences, vol.108, issue.51, pp.20311-20316, 2011.
DOI : 10.1073/pnas.1100266108

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

P. Hingamp, N. Grimsley, S. Acinas, C. Clerissi, L. Subirana et al., Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes, The ISME Journal, vol.37, issue.9, pp.1678-1695, 2013.
DOI : 10.1186/1743-422X-9-161

URL : https://hal.archives-ouvertes.fr/hal-01258223

A. Hua-van, L. Rouzic, A. Boutin, T. Filee, J. Capy et al., The struggle for life of the genome's selfish architects, Biology Direct, vol.6, issue.1, p.19, 2011.
DOI : 10.1534/genetics.105.051714

K. Inouye, S. Tanimoto, M. Kamimoto, T. Shimamoto, and T. Shimamoto, Two novel retron elements are replaced with retron-Vc95 in Vibrio cholerae, Microbiology and Immunology, vol.87, issue.7, pp.510-513, 2011.
DOI : 10.1111/j.1348-0421.2011.00342.x

P. Jaillon, C. Chica, E. Novoa, P. Hingamp, E. Pelletier et al., Marine plankton reveal a large unknown portion of the eukaryotic gene repertoire

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.462-467, 2005.
DOI : 10.1159/000084979

V. Kapitonov, S. Tempel, and J. Jurka, Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences, Gene, vol.448, issue.2, pp.207-213, 2009.
DOI : 10.1016/j.gene.2009.07.019

E. Karsenti, S. Acinas, P. Bork, C. Bowler, D. Vargas et al., A Holistic Approach to Marine Eco-Systems Biology, PLoS Biology, vol.6, issue.10, p.1001177, 2011.
DOI : 10.1371/journal.pbio.1001177.g002

URL : https://hal.archives-ouvertes.fr/hal-00691580

P. Keeling, F. Burki, H. Wilcox, B. Allam, E. Allen et al., The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing, PLoS Biology, vol.9, issue.6, p.1001889, 2014.
DOI : 10.1371/journal.pbio.1001889.s001

URL : https://hal.archives-ouvertes.fr/hal-01109521

H. Khan, C. Kozera, B. Curtis, J. Bussey, S. Theophilou et al., Retrotransposons and Tandem Repeat Sequences in the Nuclear Genomes of Cryptomonad Algae, Journal of Molecular Evolution, vol.14, issue.Suppl, pp.223-236, 2007.
DOI : 10.1007/s00239-006-0088-9

K. Kojima and H. Fujiwara, An extraordinary retrotransposon family encoding dual endonucleases, Genome Research, vol.15, issue.8, pp.1106-1117, 2005.
DOI : 10.1101/gr.3271405

K. Kojima and M. Kanehisa, Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture, Molecular Biology and Evolution, vol.25, issue.7, pp.1395-1404, 2008.
DOI : 10.1093/molbev/msn081

I. Korf, Gene finding in novel genomes, BMC Bioinformatics, vol.5, issue.1, p.59, 2004.
DOI : 10.1186/1471-2105-5-59

M. Krom, N. Kress, S. Brenner, and L. Gordon, Phosphorus limitation of primary productivity in the eastern Mediterranean Sea, Limnology and Oceanography, vol.36, issue.3, pp.424-432, 1991.
DOI : 10.4319/lo.1991.36.3.0424

J. Labonte, E. Field, M. Lau, D. Chivian, E. Van-heerden et al., Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population, Frontiers in Microbiology, vol.6, p.349, 2015.
DOI : 10.3389/fmicb.2015.00349

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

G. Lima-mendez, K. Faust, N. Henry, J. Decelle, C. S. Carcillo et al., Determinants of community structure in the global plankton interactome, Science, vol.348, issue.6237, p.1262073, 2015.
DOI : 10.1126/science.1262073

URL : https://hal.archives-ouvertes.fr/hal-01234200

C. Llorens, R. Futami, L. Covelli, L. Dominguez-escriba, J. Viu et al., The Gypsy Database (GyDB) of mobile genetic elements: release 2.0, Nucleic Acids Research, vol.39, issue.Database, pp.70-74, 2011.
DOI : 10.1093/nar/gkq1061

H. Lorenzi, M. Thiagarajan, B. Haas, J. Wortman, N. Hall et al., Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species, BMC Genomics, vol.9, issue.1, p.595, 2008.
DOI : 10.1186/1471-2164-9-595

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, vol.1, issue.1, p.18, 2012.
DOI : 10.1186/2047-217X-1-18

URL : http://doi.org/10.1186/2047-217x-1-18

A. Marchler-bauer, C. Zheng, F. Chitsaz, M. Derbyshire, L. Geer et al., CDD: conserved domains and protein three-dimensional structure, Nucleic Acids Research, vol.41, issue.D1, pp.348-352, 2013.
DOI : 10.1093/nar/gks1243

URL : http://doi.org/10.1093/nar/gks1243

F. Maumus, A. 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, issue.1, p.624, 2009.
DOI : 10.1186/1471-2164-10-624

B. Medhekar and J. Miller, Diversity-generating retroelements, Current Opinion in Microbiology, vol.10, issue.4, pp.388-395, 2007.
DOI : 10.1016/j.mib.2007.06.004

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703298

J. Miller, L. Coq, J. Hodes, A. Barbalat, R. Miller et al., Selective Ligand Recognition by a Diversity-Generating Retroelement Variable Protein, PLoS Biology, vol.72, issue.6, p.131, 2008.
DOI : 10.1371/journal.pbio.0060131.st003

H. Moreau, B. Verhelst, A. Couloux, E. Derelle, S. Rombauts et al., Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage, Genome Biology, vol.13, issue.8, p.74, 2012.
DOI : 10.1126/science.1188800

H. Noguchi, J. Park, and T. Takagi, MetaGene: prokaryotic gene finding from environmental genome shotgun sequences, Nucleic Acids Research, vol.34, issue.19, pp.5623-5630, 2006.
DOI : 10.1093/nar/gkl723

J. Oksanen, R. Kindt, P. Legendre, O. Hara, B. Stevens et al., The vegan package, 2007.

L. Orgel and F. Crick, Selfish DNA: the ultimate parasite, Nature, vol.16, issue.5757, pp.604-607, 1980.
DOI : 10.1038/284604a0

B. Palenik, J. Grimwood, A. Aerts, P. Rouze, A. Salamov et al., The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation, Proceedings of the National Academy of Sciences, vol.104, issue.18, pp.7705-7710, 2007.
DOI : 10.1073/pnas.0611046104

S. Pesant, F. Not, M. Picheral, S. Kandels-lewis, L. Bescot et al., Open science resources for the discovery and analysis of Tara Oceans data, p.150023, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01253984

M. Piednoel, T. Donnart, C. Esnault, P. Graca, D. Higuet et al., LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements, PLoS ONE, vol.19, issue.3, p.57675, 2013.
DOI : 10.1371/journal.pone.0057675.s005

M. Rho, S. Schaack, X. Gao, S. Kim, M. Lynch et al., LTR retroelements in the genome of Daphnia pulex, BMC Genomics, vol.11, issue.1, p.425, 2010.
DOI : 10.1186/1471-2164-11-425

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

J. Riordan and A. Dupuy, Domesticated transposable element gene products in human cancer, Mobile Genetic Elements, vol.63, issue.5, p.26693, 2013.
DOI : 10.1146/annurev-genet-110711-155621

P. Schnable, D. Ware, R. Fulton, J. Stein, F. Wei et al., The B73 Maize Genome: Complexity, Diversity, and Dynamics, Science, vol.326, issue.5956, pp.1112-1115, 2009.
DOI : 10.1126/science.1178534

URL : https://hal.archives-ouvertes.fr/hal-00751527

D. Simon and S. Zimmerly, A diversity of uncharacterized reverse transcriptases in bacteria, Nucleic Acids Research, vol.36, issue.22, pp.7219-7229, 2008.
DOI : 10.1093/nar/gkn867

I. Siokou-frangou, U. Christaki, M. Mazzocchi, M. Montresor, M. Ribera-d-'alcalá et al., Plankton in the open Mediterranean Sea: a review, Biogeosciences, vol.7, issue.5, pp.1543-1586, 2010.
DOI : 10.5194/bg-7-1543-2010

URL : https://hal.archives-ouvertes.fr/hal-00767891

M. Siomi, K. Sato, D. Pezic, and A. Aravin, PIWI-interacting small RNAs: the vanguard of genome defence, Nature Reviews Molecular Cell Biology, vol.103, issue.4, pp.246-258, 2011.
DOI : 10.1038/nrm3089

R. Slotkin and R. Martienssen, Transposable elements and the epigenetic regulation of the genome, Nature Reviews Genetics, vol.3, issue.4, pp.272-285, 2007.
DOI : 10.1038/nrg2072

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2729, 2013.
DOI : 10.1093/molbev/mst197

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840312

I. Teneng, V. Stribinskis, and K. Ramos, Context-specific regulation of LINE-1, Genes to Cells, vol.33, issue.10, pp.1101-1110, 2007.
DOI : 10.1007/s11626-998-0060-7

N. Toro and R. Nisa-martinez, Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases, PLoS ONE, vol.13, issue.9, p.114083, 2014.
DOI : 10.1371/journal.pone.0114083.s002

T. Watanabe, T. Nozawa, C. Aikawa, A. Amano, F. Maruyama et al., CRISPR Regulation of Intraspecies Diversification by Limiting IS Transposition and Intercellular Recombination, Genome Biology and Evolution, vol.5, issue.6, pp.1099-1114, 2013.
DOI : 10.1093/gbe/evt075

T. Wicker, F. Sabot, A. Hua-van, J. 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

J. Wootton, Non-globular domains in protein sequences: Automated segmentation using complexity measures, Computers & Chemistry, vol.18, issue.3, pp.269-285, 1994.
DOI : 10.1016/0097-8485(94)85023-2

D. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107