Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system, Nature, vol.394, pp.744-751, 1998. ,
An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms, Current Opinion in Plant Biology, vol.9, issue.3, pp.264-273, 2006. ,
DOI : 10.1016/j.pbi.2006.03.013
A Novel Polyubiquitin Structure in Cercozoa and Foraminifera: Evidence for a New Eukaryotic Supergroup, Molecular Biology and Evolution, vol.20, issue.1, pp.62-66, 2003. ,
DOI : 10.1093/molbev/msg006
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism, Science, vol.306, pp.79-86, 2004. ,
Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes, BMC Evolutionary Biology, vol.8, issue.1, p.203, 2008. ,
DOI : 10.1186/1471-2148-8-203
The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, vol.456, pp.239-244, 2008. ,
URL : https://hal.archives-ouvertes.fr/cea-00910244
A mesoscale phytoplankton bloom in the polar Southern Ocean stimulated by iron fertilization, Nature, vol.407, pp.695-702, 2000. ,
Stress and transposable elements: co-evolution or useful parasites?, Heredity, vol.9, issue.2, pp.101-106, 2000. ,
DOI : 10.1093/nar/24.23.4825
The Southern Ocean Biological Response to Aeolian Iron Deposition, Science, vol.317, issue.5841, pp.1067-1070, 2007. ,
DOI : 10.1126/science.1144602
The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa., International Journal of Systematic and Evolutionary Microbiology, vol.52, issue.2, pp.297-354, 2002. ,
DOI : 10.1099/00207713-52-2-297
DNA modification of a maize transposable element correlates with loss of activity., Proceedings of the National Academy of Sciences, vol.83, issue.6, pp.1767-1771, 1986. ,
DOI : 10.1073/pnas.83.6.1767
RNA from the 5' end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site, Proceedings of the National Academy of Sciences, vol.103, issue.47, pp.17602-17607, 2006. ,
DOI : 10.1073/pnas.0605476103
Genome analysis of the smallest free-living eukaryote ,
URL : https://hal.archives-ouvertes.fr/hal-00164247
The highly reduced genome of an enslaved algal nucleus, Nature, vol.410, pp.1091-1096, 2001. ,
Transformation of Nonselectable Reporter Genes in Marine Diatoms, Marine Biotechnology, vol.1, issue.3, pp.239-251, 1999. ,
DOI : 10.1007/PL00011773
DNA Transposons and the Evolution of Eukaryotic Genomes, Annual Review of Genetics, vol.41, issue.1, pp.331-368, 2007. ,
DOI : 10.1146/annurev.genet.40.110405.090448
Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components, Science, vol.281, issue.5374, pp.237-240, 1998. ,
DOI : 10.1126/science.281.5374.237
Characterization of diatom???cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequences, Environmental Microbiology, vol.54, issue.11, pp.1913-1925, 2006. ,
DOI : 10.1046/j.1462-2920.2003.00451.x
Chromodomains direct integration of retrotransposons to heterochromatin, Genome Research, vol.18, issue.3, pp.359-369, 2008. ,
DOI : 10.1101/gr.7146408
Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus, Proceedings of the National Academy of Sciences, vol.103, issue.25, pp.9566-9571, 2006. ,
DOI : 10.1073/pnas.0600707103
Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes, Proceedings of the National Academy of Sciences, vol.104, issue.22, pp.9352-9357, 2007. ,
DOI : 10.1073/pnas.0702741104
Horizontal gene transfer, genome innovation and evolution, Nature Reviews Microbiology, vol.148, issue.9, pp.679-687, 2005. ,
DOI : 10.1126/science.1103289
The DIRS1 Group of Retrotransposons, Molecular Biology and Evolution, vol.18, issue.11, pp.2067-2082, 2001. ,
DOI : 10.1093/oxfordjournals.molbev.a003748
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
Patterns of Hermes transposition in Drosophila melanogaster, Mol Genet Genomics, vol.268, pp.779-790, 2003. ,
Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of Rhizaria with Chromalveolates, Molecular Biology and Evolution, vol.24, issue.8, pp.1702-1713, 2007. ,
DOI : 10.1093/molbev/msm089
Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae, Eukaryotic Cell, vol.4, issue.6, pp.1102-1115, 2005. ,
DOI : 10.1128/EC.4.6.1102-1115.2005
Nucleus-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Indicates a Single Origin for Chromalveolate Plastids, Molecular Biology and Evolution, vol.20, issue.10, pp.1730-1735, 2003. ,
DOI : 10.1093/molbev/msg195
On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.55, issue.1, pp.487-496, 2005. ,
DOI : 10.1099/ijs.0.63216-0
The diversity of LTR retrotransposons, Genome Biology, vol.5, issue.6, p.225, 2004. ,
DOI : 10.1186/gb-2004-5-6-225
Macrotransposition and Other Complex Chromosomal Restructuring in Maize by Closely Linked Transposons in Direct Orientation, THE PLANT CELL ONLINE, vol.20, issue.8, pp.2019-2032, 2008. ,
DOI : 10.1105/tpc.108.060582
Short Retroposons in Eukaryotic Genomes, International Review of Cytology, vol.247, pp.165-221, 2005. ,
DOI : 10.1016/S0074-7696(05)47004-7
Plant Retrotransposons, Annual Review of Genetics, vol.33, issue.1, pp.479-532, 1999. ,
DOI : 10.1146/annurev.genet.33.1.479
Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001. ,
Retrotransposons and retroviruses: analysis of the envelope gene, Molecular Biology and Evolution, vol.16, issue.9, pp.1198-1207, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026210
URL : https://hal.archives-ouvertes.fr/hal-00428444
The genome of the protist parasite Entamoeba histolytica, Nature, vol.21, issue.7028, pp.865-868, 2005. ,
DOI : 10.1093/bioinformatics/17.8.754
The Structure and Evolution of Penelope in the virilis Species Group of Drosophila: An Ancient Lineage of Retroelements, Journal of Molecular Evolution, vol.52, issue.5, pp.445-456, 2001. ,
DOI : 10.1007/s002390010174
Update of the Diatom EST Database: a new tool for digital transcriptomics, Nucleic Acids Research, vol.37, issue.Database, 2008. ,
DOI : 10.1093/nar/gkn905
The age and evolution of non-LTR retrotransposable elements, Molecular Biology and Evolution, vol.16, issue.6, pp.793-805, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026164
BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.), Plant Molecular Biology, vol.9, issue.5, pp.829-846, 1993. ,
DOI : 10.1007/BF00027369
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima, Nature, vol.399, pp.323-329, 1999. ,
Evolution in Action across Phylogeny Caused by Microclimatic Stresses at ???Evolution Canyon???, Theoretical Population Biology, vol.52, issue.3, pp.231-243, 1997. ,
DOI : 10.1006/tpbi.1997.1330
Biology of Mammalian L1 Retrotransposons, Annual Review of Genetics, vol.35, issue.1, pp.501-538, 2001. ,
DOI : 10.1146/annurev.genet.35.102401.091032
Gene Replacement of Fructose-1,6-Bisphosphate Aldolase Supports the Hypothesis of a Single Photosynthetic Ancestor of Chromalveolates, Eukaryotic Cell, vol.3, issue.5, pp.1169-1175, 2004. ,
DOI : 10.1128/EC.3.5.1169-1175.2004
Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses, Gene, vol.390, issue.1-2, pp.3-17, 2007. ,
DOI : 10.1016/j.gene.2006.08.008
The Origin and Establishment of the Plastid in Algae and Plants, Annual Review of Genetics, vol.41, issue.1, pp.147-168, 2007. ,
DOI : 10.1146/annurev.genet.41.110306.130134
The Complete Chloroplast Genome of the Chlorarachniophyte Bigelowiella natans: Evidence for Independent Origins of Chlorarachniophyte and Euglenid Secondary Endosymbionts, Molecular Biology and Evolution, vol.24, issue.1, pp.54-62, 2007. ,
DOI : 10.1093/molbev/msl129
Alu elements and the human genome, Genetica, vol.108, issue.1, pp.57-72, 2000. ,
DOI : 10.1023/A:1004099605261
Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome, Heredity, vol.98, issue.6, pp.381-388, 2006. ,
DOI : 10.1038/sj.hdy.6800903
The paleontology of intergene retrotransposons of maize, Nat Genet, vol.20, pp.43-45, 1998. ,
Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency, Molecular and Cellular Biology, vol.28, issue.17, pp.5543-5554, 2008. ,
DOI : 10.1128/MCB.00416-08
Evolution of the diatoms: insights from fossil, biological and molecular data, Phycologia, vol.45, issue.4, pp.361-402, 2006. ,
DOI : 10.2216/05-22.1
Molecular domestication of transposable elements: From detrimental parasites to useful host genes, Cellular and Molecular Life Sciences, vol.66, issue.6, 2009. ,
DOI : 10.1007/s00018-009-8376-3
Marine Macrophytes as a Global Carbon Sink, Science, vol.211, issue.4484, pp.838-840, 1981. ,
DOI : 10.1126/science.211.4484.838
A nuclear-encoded small-subunit ribosomal RNA timescale for diatom evolution, Marine Micropaleontology, vol.65, issue.1-2, pp.1-12, 2007. ,
DOI : 10.1016/j.marmicro.2007.05.002
Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates, Nature, vol.22, issue.6840, pp.940-944, 2001. ,
DOI : 10.1038/35082058
Rooting the Eukaryote Tree by Using a Derived Gene Fusion, Science, vol.297, issue.5578, pp.89-91, 2002. ,
DOI : 10.1126/science.1071196
The root of the eukaryote tree pinpointed, Current Biology, vol.13, issue.17, pp.665-666, 2003. ,
DOI : 10.1016/S0960-9822(03)00602-X
The Silica Balance in the World Ocean: A Reestimate, Science, vol.268, issue.5209, pp.375-379, 1995. ,
DOI : 10.1126/science.268.5209.375
Spring in the California Current:the distribution of phytoplankton species, April 1993 and April 1995, Marine Ecology Progress Series, vol.167, pp.73-88, 1993. ,
DOI : 10.3354/meps167073
Geographical variation in insertion site number of retrotransposon 412 ,
URL : https://hal.archives-ouvertes.fr/hal-00435042
Plant retrotransposons: Turned on by stress, Current Biology, vol.6, issue.8, pp.959-961, 1996. ,
DOI : 10.1016/S0960-9822(02)00638-3
Origin and evolution of retroelements based upon their reverse transcriptase sequences, EMBO J, vol.9, pp.3353-3362, 1990. ,
A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis, Proceedings of the National Academy of Sciences, vol.99, issue.18, pp.11724-11729, 2002. ,
DOI : 10.1073/pnas.172234799
A Molecular Timeline for the Origin of Photosynthetic Eukaryotes, Molecular Biology and Evolution, vol.21, issue.5, pp.809-818, 2004. ,
DOI : 10.1093/molbev/msh075
Transposition of Reversed Ac Element Ends Generates Chromosome Rearrangements in Maize, Genetics, vol.167, issue.4, pp.1929-1937, 2004. ,
DOI : 10.1534/genetics.103.026229
Transposition of Reversed Ac Element Ends Generates Novel Chimeric Genes in Maize, PLoS Genetics, vol.81, issue.10, p.164, 2006. ,
DOI : 10.1371/journal.pgen.0020164.sv001
The Genome Sequence of Drosophila melanogaster, Science, vol.287, issue.5461, pp.2185-2195, 2000. ,
DOI : 10.1126/science.287.5461.2185
The loop domain of heat shock transcription factor 1 dictates DNA-binding specificity and responses to heat stress, Genes & Development, vol.15, issue.16, pp.152134-152179, 2001. ,
DOI : 10.1101/gad.894801
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism, Science, vol.306, pp.79-86, 2004. ,
A novel DNA binding protein with homology to Myb oncoproteins containing only one repeat can function as a transcriptional activator, EMBO J, issue.22, pp.135383-92, 1994. ,
1.4 .ANG. Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore, Biochemistry, vol.34, issue.19, pp.6278-6287, 1995. ,
DOI : 10.1021/bi00019a004
The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, vol.456, pp.239-244, 2008. ,
URL : https://hal.archives-ouvertes.fr/cea-00910244
The wing in yeast heat shock transcription factor (HSF) DNA-binding domain is required for full activity, Nucleic Acids Research, vol.29, issue.8, pp.291715-291738, 2001. ,
DOI : 10.1093/nar/29.8.1715
Mouse retinoid X receptor contains a separable ligand-binding and transactivation domain in its E region., Molecular and Cellular Biology, vol.15, issue.1, pp.255-63, 1995. ,
DOI : 10.1128/MCB.15.1.255
Transcription regulation and animal diversity, Nature, vol.424, issue.6945, pp.147-151, 2003. ,
DOI : 10.1038/nature01763
One billion years of Myb, Review. Oncogene, vol.13, issue.2, pp.223-235, 1996. ,
Transcription factors 2: helix-loop-helix, Protein Profile, vol.2, pp.621-702, 1995. ,
Characterization of pco-1, a newly identified gene which regulates purine catabolism in Neurospora, Current Genetics, vol.11, issue.4, pp.213-240, 2004. ,
DOI : 10.1007/s00294-004-0530-8
Update of the Diatom EST Database: a new tool for digital transcriptomics, Nucleic Acids Research, vol.37, issue.Database, 2008. ,
DOI : 10.1093/nar/gkn905
Transcriptional regulation of heat shock genes. A paradigm for inducible genomic responses. Review, J Biol Chem, vol.267, issue.31, pp.21987-90, 1992. ,
Regulation of the heat shock transcriptional response: cross talk between a family of heat shock factors, molecular chaperones, and negative regulators, Genes & Development, vol.12, issue.24, pp.123788-96, 1998. ,
DOI : 10.1101/gad.12.24.3788
Isolation of human cDNA clones of myb-related genes, A-myb and B-myb, Nucleic Acids Res, issue.23, pp.1611075-89, 1988. ,
Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need? Cell Stress Chaperones, pp.177-89, 2001. ,
The Schizosaccharomyces pombe cdc5+ gene encodes an essential protein with homology to ,
Green Transcription Factors: A Chlamydomonas Overview, Genetics, vol.179, issue.1, pp.31-39, 2008. ,
DOI : 10.1534/genetics.107.086090
Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes, Science, vol.290, issue.5499, pp.2105-2110, 2000. ,
DOI : 10.1126/science.290.5499.2105
Java Treeview--extensible visualization of microarray data, Bioinformatics, vol.20, issue.17, 2004. ,
DOI : 10.1093/bioinformatics/bth349
Microarray Analysis of Diurnal and Circadian-Regulated Genes in Arabidopsis, THE PLANT CELL ONLINE, vol.13, issue.1, pp.113-123, 2001. ,
DOI : 10.1105/tpc.13.1.113
Regulation of the heat-shock response Plant Physiol, pp.1135-1176, 1998. ,
Yeast heat shock factor is an essential DNA-binding protein that exhibits temperature-dependent phosphorylation, Cell, vol.54, issue.6, pp.855-64, 1988. ,
DOI : 10.1016/S0092-8674(88)91219-6
New insights into the mechanism of heat shock response activation, Cellular and Molecular Life Sciences, vol.65, issue.6 ,
DOI : 10.1007/s00018-008-7458-y
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
P: CCMP -Provasoli-Guillard National Center for Culture of Marine Phytoplankton 1997 list of strains, Journal of Phycology, pp.331-75, 1997. ,
The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism, Science, vol.306, pp.79-86, 2004. ,
Do Plants Have a One-Way Ticket to Genomic Obesity? The Plant cell, pp.1509-1514, 1997. ,
The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, vol.456, pp.239-244, 2008. ,
URL : https://hal.archives-ouvertes.fr/cea-00910244
(BACILLARIOPHYCEAE), Journal of Phycology, vol.41, issue.1, pp.7-20, 2005. ,
DOI : 10.1111/j.1529-8817.2005.04052.x
DNA modification of a maize transposable element correlates with loss of activity., Proceedings of the National Academy of Sciences, vol.83, issue.6, pp.1767-1771, 1986. ,
DOI : 10.1073/pnas.83.6.1767
Transformation of Nonselectable Reporter Genes in Marine Diatoms, Marine Biotechnology, vol.1, issue.3, pp.239-251, 1999. ,
DOI : 10.1007/PL00011773
Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean, Nature, vol.387, issue.6630, pp.272-275, 1997. ,
DOI : 10.1038/387272a0
The Evolution of Modern Eukaryotic Phytoplankton, Science, vol.305, issue.5682, pp.354-360, 2004. ,
DOI : 10.1126/science.1095964
LOX-Induced Lipid Peroxidation Mechanism Responsible for the Detrimental Effect of Marine Diatoms on Zooplankton Grazers, ChemBioChem, vol.142, issue.15, pp.1810-1818, 2007. ,
DOI : 10.1002/cbic.200700269
Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata., Proceedings of the National Academy of Sciences, vol.88, issue.21, pp.9794-9798, 1991. ,
DOI : 10.1073/pnas.88.21.9794
Translational recoding signals between gag and pol in diverse LTR retrotransposons, RNA, vol.9, issue.12, pp.1422-1430, 2003. ,
DOI : 10.1261/rna.5105503
Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics, Nature, vol.337, issue.6205, pp.376-380, 1989. ,
DOI : 10.1038/337376a0
Culture of Phytoplankton for Feeding Marine Invertebrates, Culture of Marine Invertebrate Animals ,
DOI : 10.1007/978-1-4615-8714-9_3
The Temperature-Dependent Change in Methylation of the Antirrhinum Transposon Tam3 Is Controlled by the Activity of Its Transposase, THE PLANT CELL ONLINE, vol.18, issue.1, pp.104-118, 2006. ,
DOI : 10.1105/tpc.105.037655
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer, Gene, vol.73, issue.1, pp.237-244, 1988. ,
DOI : 10.1016/0378-1119(88)90330-7
Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006. ,
DOI : 10.1093/molbev/msj030
Aldehyde suppression of copepod recruitment in blooms of a ubiquitous planktonic diatom, Nature, vol.198, issue.6990, pp.403-407, 2004. ,
DOI : 10.1006/abio.1995.1353
GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants, EMBO J, vol.6, pp.3901-3907, 1987. ,
Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence, Proceedings of the National Academy of Sciences, vol.97, issue.12, pp.6603-6607, 2000. ,
DOI : 10.1073/pnas.110587497
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective, Genome Biol, vol.3, p.84, 2002. ,
Molecular paleontology of transposable elements in the Drosophila melanogaster genome, Proceedings of the National Academy of Sciences, vol.100, issue.11, pp.6569-6574, 2003. ,
DOI : 10.1073/pnas.0732024100
Transposons and an Ancient HARBI1 Gene Derived from a Transposase, DNA and Cell Biology, vol.23, issue.5, pp.311-324, 2004. ,
DOI : 10.1089/104454904323090949
Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence, Genome Res, vol.8, pp.464-478, 1998. ,
Analysis of an osmotic stress induced cDNA library of the psychrophilic diatom Fragilariopsis cylindrus, 2004. ,
Plant Retrotransposons, Annual Review of Genetics, vol.33, issue.1, pp.479-532, 1999. ,
DOI : 10.1146/annurev.genet.33.1.479
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Briefings in Bioinformatics, vol.5, issue.2, pp.150-163, 2004. ,
DOI : 10.1093/bib/5.2.150
Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001. ,
Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions, TAG Theoretical and Applied Genetics, vol.109, issue.1, pp.200-209, 2004. ,
DOI : 10.1007/s00122-004-1618-8
Update of the Diatom EST Database: a new tool for digital transcriptomics, Nucleic Acids Research, vol.37, issue.Database, 2008. ,
DOI : 10.1093/nar/gkn905
Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis, Nature, vol.15, issue.6834, pp.212-214, 2001. ,
DOI : 10.1038/35075612
Empirical relationship between the number of nucleotide substitutions and interspecific identity of amino acid sequences in some proteins, Journal of Molecular Evolution, vol.1, issue.4, pp.313-323, 1976. ,
DOI : 10.1007/BF01743627
Retroposons: Genetic Footprints on the Evolutionary Paths of Life ,
DOI : 10.1007/978-1-59745-581-7_13
Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis, Gene, vol.424, issue.1-2, pp.153-158, 2008. ,
DOI : 10.1016/j.gene.2008.07.021
Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum), Mol Genet Genomics, vol.278, pp.1-15, 2007. ,
Picoeukaryotic sequences in the Sargasso Sea metagenome, Genome Biology, vol.9, issue.1, p.5, 2008. ,
DOI : 10.1186/gb-2008-9-1-r5
Specific expression of the tobacco Tnt1 retrotransposon in protoplasts, EMBO J, vol.10, pp.1911-1918, 1991. ,
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
The evolution of silicification in diatoms: inescapable sinking and sinking as escape? New Phytologist, pp.45-61, 2004. ,
Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes, Aquatic Toxicology, vol.85, issue.3, pp.219-227, 2007. ,
DOI : 10.1016/j.aquatox.2007.09.006
Age and nutrient limitation enhance polyunsaturated aldehyde production in marine diatoms, Phytochemistry, vol.68, issue.15, pp.2059-2067, 2007. ,
DOI : 10.1016/j.phytochem.2007.05.012
G: The Diatoms: Biology and Morphology of the Genera, 1990. ,
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific, PLoS Biol, vol.5, p.77, 2007. ,
The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-425, 1987. ,
The paleontology of intergene retrotransposons of maize, Nat Genet, vol.20, pp.43-45, 1998. ,
Nested retrotransposons in the intergenic regions of the maize genome, Science, vol.274, pp.765-768, 1996. ,
Genome Properties of the Diatom Phaeodactylum tricornutum, PLANT PHYSIOLOGY, vol.129, issue.3, pp.993-1002, 2002. ,
DOI : 10.1104/pp.010713
Somatic Excision of the Ac Transposable Element in Transgenic Arabidopsis thaliana after 5-Azacytidine Treatment, Plant and Cell Physiology, vol.38, issue.3, pp.336-343, 1997. ,
DOI : 10.1093/oxfordjournals.pcp.a029171
A Diatom Gene Regulating Nitric-Oxide Signaling and Susceptibility to Diatom-Derived Aldehydes, Current Biology, vol.18, issue.12, pp.895-899, 2008. ,
DOI : 10.1016/j.cub.2008.05.037
A Stress Surveillance System Based on Calcium and Nitric Oxide in Marine Diatoms, PLoS Biology, vol.37, issue.3, p.60, 2006. ,
DOI : 10.1371/journal.pbio.0040060.sv001
Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science, vol.304, issue.5667, pp.66-74, 2004. ,
DOI : 10.1126/science.1093857
Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum, THE PLANT CELL ONLINE, vol.11, issue.9, pp.1769-1784, 1999. ,
DOI : 10.1105/tpc.11.9.1769
Plant retrotransposons: Turned on by stress, Current Biology, vol.6, issue.8, pp.959-961, 1996. ,
DOI : 10.1016/S0960-9822(02)00638-3
Origin and evolution of retroelements based upon their reverse transcriptase sequences, EMBO J, vol.9, pp.3353-3362, 1990. ,
MOLECULAR BIOLOGY: Amplified Silencing, Science, vol.315, issue.5809, pp.199-200, 2007. ,
DOI : 10.1126/science.1138030
Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells, Journal of Molecular Biology, vol.203, issue.4, pp.971-983, 1988. ,
DOI : 10.1016/0022-2836(88)90122-2
On the origin and functions of RNA-mediated silencing: from protists to man, Current Genetics, vol.299, issue.2, pp.81-99, 2006. ,
DOI : 10.1007/s00294-006-0078-x
Structure and Function of Eukaryotic DNA Methyltransferases, Curr Top Dev Biol, vol.60, pp.55-89, 2004. ,
DOI : 10.1016/S0070-2153(04)60003-2
AdoMet-dependent methylation, DNA methyltransferases and base flipping, Nucleic Acids Research, vol.29, issue.18, pp.3784-3795, 2001. ,
DOI : 10.1093/nar/29.18.3784
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature, vol.452, pp.215-219, 2008. ,
Transformation of Nonselectable Reporter Genes in Marine Diatoms, Marine Biotechnology, vol.1, issue.3, pp.239-251, 1999. ,
DOI : 10.1007/PL00011773
Imprinting and the Epigenetic Asymmetry Between Parental Genomes, Science, vol.293, issue.5532, pp.1086-1089, 2001. ,
DOI : 10.1126/science.1064020
Double chromodomains cooperate to recognize the methylated histone H3 tail, Nature, vol.12, issue.7071, pp.1181-1185, 2005. ,
DOI : 10.1038/nature04290
Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the pattern of DNA methylation, Nat Genet, vol.24, pp.368-371, 2000. ,
An Inside Job for siRNAs, Molecular Cell, vol.31, issue.3, pp.309-312, 2008. ,
DOI : 10.1016/j.molcel.2008.07.008
EUKARYOTIC CYTOSINE METHYLTRANSFERASES, Annual Review of Biochemistry, vol.74, issue.1, pp.481-514, 2005. ,
DOI : 10.1146/annurev.biochem.74.010904.153721
Methylation of tRNAAsp by the DNA Methyltransferase Homolog Dnmt2, Science, vol.311, issue.5759, pp.395-398, 2006. ,
DOI : 10.1126/science.1120976
piRNAs--the ancient hunters of genome invaders, Genes & Development, vol.21, issue.14, pp.1707-1713, 2007. ,
DOI : 10.1101/gad.1567007
DNA modification mechanisms and gene activity during development, Science, vol.187, issue.4173, pp.226-232, 1975. ,
DOI : 10.1126/science.1111098
Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006. ,
DOI : 10.1093/molbev/msj030
Argonaute proteins: key players in RNA silencing, Nature Reviews Molecular Cell Biology, vol.13, issue.1, pp.22-32, 2008. ,
DOI : 10.1038/nrm2321
Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals, Nature Genetics, vol.33, issue.3s, pp.245-254, 2003. ,
DOI : 10.1038/ng1089
DNA NUCLEOSIDE COMPOSITION AND METHYLATION IN SEVERAL SPECIES OF MICROALGAE1, Journal of Phycology, vol.28, issue.3, pp.356-362, 1992. ,
DOI : 10.1111/j.0022-3646.1992.00356.x
Maintenance of genomic methylation requires a SWI2/SNF2-like protein, Nat Genet, vol.22, pp.94-97, 1999. ,
Cancer epigenetics comes of age, Nature Genetics, vol.21, issue.2, pp.163-167, 1999. ,
DOI : 10.1038/5947
The Role of DNA Methylation in Mammalian Epigenetics, Science, vol.293, issue.5532, pp.1068-1070, 2001. ,
DOI : 10.1126/science.1063852
Roles of JUMONJI in mouse embryonic development, Developmental Dynamics, vol.110, issue.1, pp.21-32, 2005. ,
DOI : 10.1002/dvdy.20204
and chromo domains gauge the degree of lysine methylation, EMBO Rep, vol.7, pp.397-403, 2006. ,
Chromatin Modifications and Their Function, Cell, vol.128, issue.4, pp.693-705, 2007. ,
DOI : 10.1016/j.cell.2007.02.005
The DNA (cytosine-5) methyltransferases, Nucleic Acids Research, vol.22, issue.1, pp.1-10, 1994. ,
DOI : 10.1093/nar/22.1.1
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality, Cell, vol.69, issue.6, pp.915-926, 1992. ,
DOI : 10.1016/0092-8674(92)90611-F
Profiling DNA methylation patterns using genomic tiling microarrays, Nature Methods, vol.12, issue.3, pp.219-224, 2005. ,
DOI : 10.1126/science.1095989
The role of RNA interference in heterochromatic silencing, Nature, vol.161, issue.7006, pp.364-370, 2004. ,
DOI : 10.1016/0092-8674(94)90119-8
Structural Basis for Double-Stranded RNA Processing by Dicer, Science, vol.311, issue.5758, pp.195-198, 2006. ,
DOI : 10.1126/science.1121638
Suppression of crossing-over by DNA methylation in??Ascobolus, Genes & Development, vol.12, issue.9 ,
DOI : 10.1101/gad.12.9.1381
RNA-mediated chromatin-based silencing in plants, Current Opinion in Cell Biology, vol.21, issue.3, 2009. ,
DOI : 10.1016/j.ceb.2009.01.025
Targets of RNA-directed DNA methylation, Current Opinion in Plant Biology, vol.10, issue.5, pp.512-519, 2007. ,
DOI : 10.1016/j.pbi.2007.06.007
Revealing the world of RNA interference, Nature, vol.567, issue.7006, pp.338-342, 2004. ,
DOI : 10.1038/415810a
Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis, Nature, vol.15, issue.6834, pp.212-214, 2001. ,
DOI : 10.1038/35075612
A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase, Genes & Development, vol.19, issue.1, pp.77-89, 2005. ,
DOI : 10.1101/gad.1265105
LSH Cooperates with DNA Methyltransferases To Repress Transcription, Molecular and Cellular Biology, vol.28, issue.1 ,
DOI : 10.1128/MCB.01073-07
Bypassing genomic imprinting allows seed development, Nature, vol.46, issue.7142, pp.312-315, 2007. ,
DOI : 10.1038/nature05770
Phosphorylation of histone H3: a balancing act between chromosome condensation and transcriptional activation, Trends in Genetics, vol.20, issue.4, pp.214-220, 2004. ,
DOI : 10.1016/j.tig.2004.02.007
Evolutionary Diversification of DNA Methyltransferases in Eukaryotic Genomes, Molecular Biology and Evolution, vol.22, issue.4, pp.1119-1128, 2005. ,
DOI : 10.1093/molbev/msi098
X inactivation, differentiation, and DNA methylation, Cytogenetic and Genome Research, vol.14, issue.1, pp.9-25, 1975. ,
DOI : 10.1159/000130315
Multivalent engagement of chromatin modifications by linked binding modules, Nature Reviews Molecular Cell Biology, vol.281, issue.12, pp.983-994, 2007. ,
DOI : 10.1038/nrm2298
Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion?, Trends in Genetics, vol.13, issue.8, pp.296-301, 1997. ,
DOI : 10.1016/S0168-9525(97)01201-8
The methylated component of the Neurospora crassa genome, Nature, vol.422, issue.6934, pp.893-897, 2003. ,
DOI : 10.1038/nature01564
An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei, RNA, vol.12, issue.12, pp.2063-2072, 2006. ,
DOI : 10.1261/rna.246906
Histone Demethylation Mediated by the Nuclear Amine Oxidase Homolog LSD1, Cell, vol.119, issue.7, pp.941-953, 2004. ,
DOI : 10.1016/j.cell.2004.12.012
Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array ,
Acetylation of Histones and Transcription-Related Factors, Microbiology and Molecular Biology Reviews, vol.64, issue.2, pp.435-459, 2000. ,
DOI : 10.1128/MMBR.64.2.435-459.2000
L3MBTL1, a histone-methylation-dependent chromatin lock, Cell, vol.129, pp.915-928, 2007. ,
Endogenous trans-Acting siRNAs Regulate the Accumulation of Arabidopsis mRNAs, Molecular Cell, vol.16, issue.1, pp.69-79, 2004. ,
DOI : 10.1016/j.molcel.2004.09.028
Knockdown stands up, Trends in Biotechnology, vol.21, issue.1, pp.2-4, 2003. ,
DOI : 10.1016/S0167-7799(02)00002-1
Human PAD4 Regulates Histone Arginine Methylation Levels via Demethylimination, Science, vol.306, issue.5694, pp.279-283, 2004. ,
DOI : 10.1126/science.1101400
Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails, Genes & Development, vol.15, issue.18, pp.2343-2360, 2001. ,
DOI : 10.1101/gad.927301
A developmental view of microRNA function, Trends in Biochemical Sciences, vol.32, issue.4, pp.189-197, 2007. ,
DOI : 10.1016/j.tibs.2007.02.006
The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses, BMC Evolutionary Biology, vol.8, issue.1, p.110, 2008. ,
DOI : 10.1186/1471-2148-8-110
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
DOI : 10.1093/nar/gkh340
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer, Gene, vol.73, issue.1, pp.237-244, 1988. ,
DOI : 10.1016/0378-1119(88)90330-7
Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006. ,
DOI : 10.1093/molbev/msj030
Large Retrotransposon Derivatives: Abundant, Conserved but Nonautonomous Retroelements of Barley and Related Genomes, Genetics, vol.166, issue.3, pp.1437-1450, 2004. ,
DOI : 10.1534/genetics.166.3.1437
Viruses in Marine Brown Algae, In Advances in Virus Research, vol.50, issue.1998, pp.49-67 ,
DOI : 10.1016/S0065-3527(08)60805-2
(ECTOCARPALES, PHAEOPHYCEAE) AS A MODEL ORGANISM FOR BROWN ALGAL GENETICS AND GENOMICS, Journal of Phycology, vol.40, issue.6, pp.1079-1088, 2004. ,
DOI : 10.1111/j.1529-8817.2004.04058.x
Inheritance of organelles in artificial hybrids of the isogamous multicellular chromist alga Ectocarpus siliculosus (Phaeophyceae) ,
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
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
Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes, Proceedings of the National Academy of Sciences, vol.98, issue.24, pp.13778-13783, 2001. ,
DOI : 10.1073/pnas.241341898
Conclusions and perspectives References: 1, Chapter ,
The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, vol.456, pp.239-244, 2008. ,
URL : https://hal.archives-ouvertes.fr/cea-00910244
Gene silencing in the marine diatom Phaeodactylum tricornutum, Nucleic Acids Research, vol.37, issue.14, 2009. ,
DOI : 10.1093/nar/gkp448