C. B. Field, M. J. Behrenfeld, J. T. Randerson, and P. Falkowski, Primary production of the biosphere: integrating terrestrial and oceanic components, Science, vol.281, pp.237-240, 1998.

S. Malviya, Insights into global diatom distribution and diversity in the world's ocean, Proceedings of the National Academy of Sciences of the United States of America, 2016.

C. De-vargas, Eukaryotic plankton diversity in the sunlit ocean, Science, vol.348, p.1261605, 2015.

C. Bowler, A. Vardi, and A. E. Allen, Oceanographic and biogeochemical insights from diatom genomes, Ann Rev Mar Sci, vol.2, pp.333-365, 2010.

L. Tirichine, A. Rastogi, and C. Bowler, Recent progress in diatom genomics and epigenomics, Curr Opin Plant Biol, vol.36, pp.46-55, 2017.

S. Basu, Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom, New Phytol, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01607004

C. Bowler, 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

E. V. Armbrust, The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism, Science, vol.306, pp.79-86, 2004.

A. Moustafa, Genomic footprints of a cryptic plastid endosymbiosis in diatoms, Science, vol.324, pp.1724-1726, 2009.

R. G. Dorrell, Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome, Elife, vol.6, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01526828

P. Deschamps and D. Moreira, Reevaluating the green contribution to diatom genomes, Genome biology and evolution, vol.4, pp.683-688, 2012.

C. Ku, Endosymbiotic origin and differential loss of eukaryotic genes, Nature, vol.524, pp.427-432, 2015.

A. Gruber, G. Rocap, P. G. Kroth, E. V. Armbrust, and T. Mock, Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage, Plant J, vol.81, pp.519-528, 2015.

U. Maheswari, Digital expression profiling of novel diatom transcripts provides insight into their biological functions, Genome biology, vol.11, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00627911

A. Veluchamy, An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum, Genome biology, vol.16, 2015.

A. Veluchamy, Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum, Nat Commun, vol.4, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01545322

D. Jangam, C. Feschotte, and E. Betran, Transposable Element Domestication As an Adaptation to Evolutionary Conflicts, Trends in genetics: TIG, vol.33, pp.817-831, 2017.

, SCIENtIfIC REPORTS |, vol.8, p.4834, 2018.

P. J. Keeling, The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing, PLoS Biol, vol.12, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01109521

W. F. Loomis, G. Shaulsky, and N. Wang, Histidine kinases in signal transduction pathways of eukaryotes, J Cell Sci, vol.110, pp.1141-1145, 1997.

E. Lee, Web Apollo: a web-based genomic annotation editing platform, Genome biology, vol.14, 2013.

S. M. Adl, The Revised Classification of Eukaryotes, Journal of Eukaryotic Microbiology, vol.59, pp.429-493, 2012.
URL : https://hal.archives-ouvertes.fr/mnhn-02498504

M. V. Omelchenko, Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance, BMC evolutionary biology, vol.5, 2005.

H. Qiu, H. S. Yoon, and D. Bhattacharya, Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes, Front Plant Sci, vol.4, 2013.

A. Moustafa, Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms, Science, vol.324, pp.1724-1726, 2009.

S. G. Gornik, Loss of Nucleosomal DNA Condensation Coincides with Appearance of a Novel Nuclear Protein in Dinoflagellates, Current Biology, vol.22, pp.2303-2312, 2012.

T. Yurchenko, T. Sevcikova, H. Strnad, A. Butenko, and M. Elias, The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite, Open Biology, vol.6, 2016.

P. J. Keeling and J. D. Palmer, Horizontal gene transfer in eukaryotic evolution, Nature Reviews Genetics, vol.9, pp.605-618, 2008.

J. S. Bernardes, F. R. Vieira, L. M. Costa, and G. Zaverucha, Evaluation and improvements of clustering algorithms for detecting remote homologous protein families, BMC bioinformatics, vol.16, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01143450

J. S. Bernardes, F. R. Vieira, G. Zaverucha, and A. Carbone, A multi-objective optimization approach accurately resolves protein domain architectures, Bioinformatics, vol.32, pp.345-353, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01285556

J. Bernardes, G. Zaverucha, C. Vaquero, and A. Carbone, Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence, PLoS Comput Biol, vol.12, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01390566

M. Lescot, Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages, ISME J, vol.10, pp.1134-1146, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01258212

E. B. Chuong, N. C. Elde, and C. Feschotte, Regulatory activities of transposable elements: from conflicts to benefits, Nature reviews. Genetics, vol.18, pp.71-86, 2017.

J. H. Laity, B. M. Lee, and P. E. Wright, Zinc finger proteins: new insights into structural and functional diversity, Current opinion in structural biology, vol.11, pp.39-46, 2001.

S. G. Sedgwick and S. J. Smerdon, The ankyrin repeat: a diversity of interactions on a common structural framework, Trends Biochem Sci, vol.24, pp.311-316, 1999.

R. Taujale and Y. Yin, Glycosyltransferase family 43 is also found in early eukaryotes and has three subfamilies in Charophycean green algae, PloS one, vol.10, 2015.

B. Baiet, N-glycans of Phaeodactylum tricornutum diatom and functional characterization of its N-acetylglucosaminyltransferase I enzyme, J Biol Chem, vol.286, pp.6152-6164, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01848363

D. C. Bassham and J. L. Crespo, Autophagy in plants and algae, Front Plant Sci, vol.5, 2014.

M. A. Bromke, Amino Acid biosynthesis pathways in diatoms, vol.3, pp.294-311, 2013.

A. M. Mcguire, M. D. Pearson, D. E. Neafsey, and J. E. Galagan, Cross-kingdom patterns of alternative splicing and splice recognition, Genome biology, vol.9, 2008.

J. E. Stajich, F. S. Dietrich, and S. W. Roy, Comparative genomic analysis of fungal genomes reveals intron-rich ancestors, Genome biology, vol.8, 2007.

A. L. Rastogi, X. Lombard, and B. Loew, Tirichine, D. & Probing, L. the evolutionary history of epigenetic mechanisms: What can we learn from marine diatoms, AIMS Genetics, vol.2, pp.173-191, 2015.

T. Mock, Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus, Nature, vol.541, pp.536-540, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01587937

E. V. Armbrust, The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism, Science, vol.306, pp.79-86, 2004.

Q. Zhang and S. V. Edwards, The evolution of intron size in amniotes: a role for powered flight?, Genome biology and evolution, vol.4, pp.1033-1043, 2012.

E. Waltari and S. V. Edwards, Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs, Am Nat, vol.160, pp.539-552, 2002.

U. Braunschweig, Widespread intron retention in mammals functionally tunes transcriptomes, Genome Res, vol.24, pp.1774-1786, 2014.

D. Vaulot, R. J. Olson, S. Merkel, and S. W. Chisholm, Cell-Cycle Response to Nutrient Starvation in 2 Phytoplankton Species, Thalassiosira-Weissflogii and Hymenomonas-Carterae, Marine Biology, vol.95, pp.625-630, 1987.

N. L. Hockin, T. Mock, F. Mulholland, S. Kopriva, and G. Malin, The Response of Diatom Central Carbon Metabolism to Nitrogen Starvation Is Different from That of Green Algae and Higher Plants, Plant Physiology, vol.158, p.184333, 2012.

F. Maumus, Potential impact of stress activated retrotransposons on genome evolution in a marine diatom, BMC genomics, vol.10, 2009.

W. Wang and E. F. Kirkness, Short interspersed elements (SINEs) are a major source of canine genomic diversity, Genome Res, vol.15, pp.1798-1808, 2005.

D. A. Kramerov and N. S. Vassetzky, Origin and evolution of SINEs in eukaryotic genomes, Heredity (Edinb), vol.107, pp.487-495, 2011.

T. N. Le, Y. Miyazaki, S. Takuno, and H. Saze, Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana, Nucleic acids research, vol.43, pp.3911-3921, 2015.

T. D. Wu and S. Nacu, Fast and SNP-tolerant detection of complex variants and splicing in short reads, Bioinformatics, vol.26, pp.873-881, 2010.

P. J. Kersey, Ensembl Genomes 2016: more genomes, more complexity, Nucleic acids research, vol.44, pp.574-580, 2016.

B. D. Ondov, A. Varadarajan, K. D. Passalacqua, and N. H. Bergman, Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications, Bioinformatics, vol.24, pp.2776-2777, 2008.

C. Trapnell, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, SCIENtIfIC REPORTS |, vol.7, pp.562-578, 2012.

B. E. Suzek, UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches, Bioinformatics, vol.31, pp.926-932, 2015.

I. Korf, Gene finding in novel genomes, BMC bioinformatics, vol.5, 2004.

M. Stanke and S. Waack, Gene prediction with a hidden Markov model and a new intron submodel, Bioinformatics, vol.19, issue.2, pp.215-225, 2003.

C. Holt and M. Yandell, MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects, BMC bioinformatics, vol.12, 2011.

S. Hunter, InterPro: the integrative protein signature database, Nucleic acids research, vol.37, pp.211-215, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01214141

M. Ruffier, Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation, Database, 2017.

B. Gschloessl, Y. Guermeur, and J. M. Cock, HECTAR: a method to predict subcellular targeting in heterokonts, BMC bioinformatics, vol.9, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00359779

J. T. Huff and D. Zilberman, Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes, Cell, vol.156, pp.1286-1297, 2014.

L. Jourdren, M. Bernard, M. A. Dillies, and S. Le-crom, Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses, Bioinformatics, vol.28, pp.1542-1543, 2012.

A. O. Marron, The Evolution of Silicon Transport in Eukaryotes, Mol Biol Evol, vol.33, pp.3226-3248, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01386826

R. Meheust, E. Zelzion, D. Bhattacharya, P. Lopez, and E. Bapteste, Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis, Proceedings of the National Academy of Sciences of the United States of America, vol.113, pp.3579-3584, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01544793

B. Langmead, Aligning short sequencing reads with Bowtie, Current protocols in bioinformatics, vol.11, pp.11-17, 2010.

T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville, Considering transposable element diversification in de novo annotation approaches, PloS one, vol.6, 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.351-358, 2005.

J. Jurka, Repbase Update, a database of eukaryotic repetitive elements, Cytogenetic and genome research, vol.110, pp.462-467, 2005.