S. Adl, A. Simpson, C. Lane, J. Lukes, D. Bass et al., The Revised Classification of Eukaryotes, Journal of Eukaryotic Microbiology, vol.56, issue.5, pp.429-493, 2012.
DOI : 10.1111/j.1550-7408.2012.00644.x

E. Armbrust, Uniparental inheritance of chloroplast genomes In The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas, Kluwer), pp.93-113, 1998.

D. Anderson, A. Cembella, and G. Hallegraeff, Progress in Understanding Harmful Algal Blooms: Paradigm Shifts and New Technologies for Research, Monitoring, and Management, Annual Review of Marine Science, vol.4, issue.1, pp.143-176, 2012.
DOI : 10.1146/annurev-marine-120308-081121

J. Archibald, The Evolution of Algae by Secondary and Tertiary Endosymbiosis, Advances in Botanical Research, vol.64, pp.87-118, 2012.
DOI : 10.1016/B978-0-12-391499-6.00003-7

H. Bik, D. L. Porazinska, S. Creer, J. Caporaso, R. Knight et al., Sequencing our way towards understanding global eukaryotic biodiversity, Trends in Ecology & Evolution, vol.27, issue.4, pp.233-243, 2012.
DOI : 10.1016/j.tree.2011.11.010

L. Bittner, A. Gobet, S. Audic, S. Romac, E. Egge et al., Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay, Molecular Ecology, vol.51, issue.1, pp.87-101, 2013.
DOI : 10.1111/mec.12108

URL : https://hal.archives-ouvertes.fr/hal-00817857

F. Burki and P. Keeling, Rhizaria, Current Biology, vol.24, issue.3, pp.103-107, 2014.
DOI : 10.1016/j.cub.2013.12.025

URL : http://doi.org/10.1016/j.cub.2013.12.025

S. Capella-gutiérrez, J. Silla-martínez, and T. Gabaldón, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1973, 2009.
DOI : 10.1093/bioinformatics/btp348

A. Chambouvet, P. Morin, D. Marie, and L. Guillou, Control of Toxic Marine Dinoflagellate Blooms by Serial Parasitic Killers, Science, vol.322, issue.5905, pp.1254-1257, 2008.
DOI : 10.1126/science.1164387

F. Chevenet, C. Brun, A. Banuls, B. Jacq, and C. R. , TreeDyn: towards dynamic graphics and annotations for analyses of trees, BMC Bioinformatics, vol.7, issue.1, p.439, 2006.
DOI : 10.1186/1471-2105-7-439

URL : https://hal.archives-ouvertes.fr/hal-00321061

J. Cole, B. Chai, R. Farris, Q. Wang, S. Kulam et al., The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis, Nucleic Acids Research, vol.33, issue.Database issue, pp.294-296, 2005.
DOI : 10.1093/nar/gki038

A. Coleman and A. Nerozzi, Temporal and Spatial Coordination of Cells with Their Plastid Component, International Review of Cytology, vol.193, pp.125-164, 1999.
DOI : 10.1016/S0074-7696(08)61780-5

C. Courties, A. Vaquer, M. Trousselier, J. Lautier, M. Chrétiennot-dinet et al., Smallest eukaryotic organism, Nature, vol.370, issue.6487, p.255, 1994.
DOI : 10.1038/370255a0

J. Decelle, I. Probert, L. Bittner, Y. Desdevises, C. S. De-vargas et al., An original mode of symbiosis in open ocean plankton, Proceedings of the National Academy of Sciences of the United States of America, pp.18000-18005, 2012.
DOI : 10.1073/pnas.1212303109

URL : https://hal.archives-ouvertes.fr/hal-01258241

T. Desantis, P. Hugenholtz, N. Larsen, M. Rojas, E. Brodie et al., Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB, Applied and Environmental Microbiology, vol.72, issue.7, pp.5069-5072, 2006.
DOI : 10.1128/AEM.03006-05

B. Edvardsen, W. Eikrem, J. Throndsen, A. Sáez, I. Probert et al., Ribosomal DNA phylogenies and a morphological revision provide the basis for a revised taxonomy of the Prymnesiales (Haptophyta), European Journal of Phycology, vol.16, issue.3, pp.202-228, 2011.
DOI : 10.1016/j.protis.2006.02.004

URL : https://hal.archives-ouvertes.fr/hal-01258244

P. Falkowski, M. Katz, A. Knoll, A. Quigg, J. Raven et al., The Evolution of Modern Eukaryotic Phytoplankton, Science, vol.305, issue.5682, pp.354-360, 2004.
DOI : 10.1126/science.1095964

N. Fuller, C. Campbell, D. Allen, F. Pitt, K. Zwirglmaier et al., Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids, Aquatic Microbial Ecology, vol.43, pp.79-93, 2006.
DOI : 10.3354/ame043079

S. Gaebler-schwarz, D. A. Assmy, P. Chen, J. Henjes, J. Nothig et al., A NEW CELL STAGE IN THE HAPLOID-DIPLOID LIFE CYCLE OF THE COLONY-FORMING HAPTOPHYTE PHAEOCYSTIS ANTARCTICA AND ITS ECOLOGICAL IMPLICATIONS1, Journal of Phycology, vol.387, issue.5, pp.1006-1016, 2010.
DOI : 10.1111/j.1529-8817.2010.00875.x

A. Godhe, M. Asplund, K. Härnström, V. Saravanan, and A. Tyagi, Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR, Applied and Environmental Microbiology, vol.74, issue.23, pp.7174-7182, 2008.
DOI : 10.1128/AEM.01298-08

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010.
DOI : 10.1093/molbev/msp259

URL : https://hal.archives-ouvertes.fr/lirmm-00705187

B. Green, Chloroplast genomes of photosynthetic eukaryotes, The Plant Journal, vol.278, issue.1, pp.34-44, 2011.
DOI : 10.1111/j.1365-313X.2011.04541.x

L. Guillou, D. Bachar, S. Audic, D. Bass, and C. Berney, The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucleic Acids Research, vol.41, issue.D1, 2012.
DOI : 10.1093/nar/gks1160

URL : https://hal.archives-ouvertes.fr/hal-01253994

M. Guiry and G. Guiry, AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. http://www.algaebase.org; searched on, 2014.
DOI : 10.1111/j.0022-3646.2003.03906001_56.x

M. Guiry, G. Guiry, L. Morrison, F. Rindi, V. Miranda et al., AlgaeBase: An On-line Resource for Algae, Cryptogamie, Algologie, vol.35, issue.2, pp.105-115, 2014.
DOI : 10.7872/crya.v35.iss2.2014.105

M. Hartmann, C. Grob, G. Tarran, A. Martina, P. Burkill et al., Mixotrophic basis of Atlantic oligotrophic ecosystems, Proceedings of the National Academy of Sciences, vol.109, issue.15, pp.5756-5760, 2012.
DOI : 10.1073/pnas.1118179109

P. Herbert, A. Cywinska, S. Ball, and J. Dewaard, Biological identifications through DNA barcodes, Proceedings of the Royal Society of London Series B-Biological Sciences, pp.313-321, 2003.

T. Hiramatsu, S. Nakamura, O. Misumi, T. Kuroiwa, and S. Nakamura, MORPHOLOGICAL CHANGES IN MITOCHONDRIAL AND CHLOROPLAST NUCLEOIDS AND MITOCHONDRIA DURING THE CHLAMYDOMONAS REINHARDTII (CHLOROPHYCEAE) CELL CYCLE, Journal of Phycology, vol.12, issue.5, pp.1048-1058, 2006.
DOI : 10.1007/BF00435691

K. Hoef-emden, Multiple Independent Losses of Photosynthesis and Differing EvolutionaryRates in the Genus Cryptomonas (Cryptophyceae): Combined Phylogenetic Analyses of DNA Sequences of the Nuclear and the Nucleomorph Ribosomal Operons, Journal of Molecular Evolution, vol.13, issue.2, pp.183-195, 2005.
DOI : 10.1007/s00239-004-0089-5

K. Hoef-emden and M. Melkonian, Revision of the Genus Cryptomonas (Cryptophyceae): a Combination of Molecular Phylogeny and Morphology Provides Insights into a Long-Hidden Dimorphism, Protist, vol.154, issue.3-4, pp.371-409, 2003.
DOI : 10.1078/143446103322454130

J. Janou?kovec, A. Horák, K. Barott, F. Rohwer, and P. Keeling, Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs, Current Biology, vol.22, issue.13, pp.518-519, 2012.
DOI : 10.1016/j.cub.2012.04.047

L. Jardillier, M. Zubkov, J. Pearman, and D. Scanlan, Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean, The ISME Journal, vol.147, issue.9, pp.1180-1192, 2010.
DOI : 10.1038/nature07236

M. Katoh and M. Kuma, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-3066, 2002.
DOI : 10.1093/nar/gkf436

L. Kermarrec, A. Franc, F. Rimet, P. Chaumeil, J. Humbert et al., Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms, Molecular Ecology Resources, vol.21, issue.4, pp.607-619, 2013.
DOI : 10.1111/1755-0998.12105

URL : https://hal.archives-ouvertes.fr/bioemco-00840234

E. Kim, J. Harrison, S. Sudek, M. Jones, H. Wilcox et al., Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life, Proceedings of the National Academy of Sciences of the United States of America, pp.1496-1500, 2011.
DOI : 10.1073/pnas.1013337108

M. Kim, S. Kim, W. Yih, and M. Park, The marine dinoflagellate genus Dinophysis can retain plastids of multiple algal origins at the same time, Harmful Algae, vol.13, pp.105-111, 2012.
DOI : 10.1016/j.hal.2011.10.010

A. Kirkham, L. Jardillier, A. Tiganescu, J. Pearman, M. Zubkov et al., Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect, Environmental Microbiology, vol.9, issue.4, pp.975-990, 2011.
DOI : 10.1111/j.1462-2920.2010.02403.x

A. Kirkham, C. Lepère, L. Jardiller, F. Not, H. Bouman et al., A global perspective on marine photosynthetic picoeukaryote community structure, The ISME Journal, vol.10, issue.5, pp.922-936, 2013.
DOI : 10.1038/nature07236

URL : https://hal.archives-ouvertes.fr/hal-00848701

A. Knoll, Paleobiological Perspectives on Early Eukaryotic Evolution, Cold Spring Harbor Perspectives in Biology, vol.6, issue.1, p.16121, 2014.
DOI : 10.1101/cshperspect.a016121

. Koumandouvl and C. Howe, The Copy Number of Chloroplast Gene Minicircles Changes Dramatically with Growth Phase in the Dinoflagellate Amphidinium operculatum, Protist, vol.158, issue.1, pp.89-103, 2007.
DOI : 10.1016/j.protis.2006.08.003

C. Lepère, D. Vaulot, and D. Scanlan, Photosynthetic picoeukaryote community structure in the South East Pacific Ocean encompassing the most oligotrophic waters on Earth, Environmental Microbiology, vol.45, issue.12, pp.3105-3117, 2009.
DOI : 10.1111/j.1462-2920.2009.02015.x

L. Lim and G. Macfadden, The evolution, metabolism and functions of the apicoplast, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.280, issue.2, pp.749-763, 2010.
DOI : 10.1016/j.chom.2008.11.001

E. Linton, A. Karnkowska-ishikawa, J. Kim, W. Shin, M. Bennett et al., Reconstructing Euglenoid Evolutionary Relationships using Three Genes: Nuclear SSU and LSU, and Chloroplast SSU rDNA Sequences and the Description of Euglenaria gen. nov. (Euglenophyta), Protist, vol.161, issue.4, pp.603-619, 2010.
DOI : 10.1016/j.protis.2010.02.002

R. Logares, S. Audic, D. Bass, L. Bittner, C. Boutte et al., Patterns of Rare and Abundant Marine Microbial Eukaryotes, Current Biology, vol.24, issue.8, pp.813-821, 2014.
DOI : 10.1016/j.cub.2014.02.050

URL : https://hal.archives-ouvertes.fr/hal-01149637

R. Logares, S. Audic, S. Santini, M. Pernice, C. De-vargas et al., Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing, The ISME Journal, vol.52, issue.10, pp.1823-1833, 2012.
DOI : 10.1016/j.femsec.2004.10.006

URL : https://hal.archives-ouvertes.fr/hal-01258237

G. Macfadden, Apicoplast, Current Biology, vol.24, issue.7, pp.262-263, 2014.
DOI : 10.1016/j.cub.2014.01.024

D. Man-aharonovich, A. Philosof, B. Kirkup, L. Gall, F. Yogev et al., Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts, The ISME Journal, vol.51, issue.8, pp.1044-1052, 2011.
DOI : 10.1016/j.femsec.2004.10.006

URL : https://hal.archives-ouvertes.fr/hal-01254019

Z. Mckie-krisberg and R. Sanders, Phagotrophy by the picoeukaryotic green alga Micromonas: implications for Arctic Oceans, The ISME Journal, vol.455, issue.10, pp.1953-1961, 2014.
DOI : 10.1038/ismej.2014.16

S. Mcdonald, D. Sarno, D. Scanlan, and A. Zingone, Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle, Aquatic Microbial Ecology, vol.50, pp.75-89, 2007.
DOI : 10.3354/ame01148

M. Montresor and L. J. , Phases, stages, and shifts in the life cycles of marine phytoplankton, Algal Cultures, Analogues of Blooms and Applications, pp.91-129, 2006.

R. Moore, M. Oborník, J. Janou?kovec, T. Chrudimsky, and M. Vancova, A photosynthetic alveolate closely related to apicomplexan parasites, Nature, vol.53, issue.7181, pp.959-963, 2008.
DOI : 10.1038/nature06635

X. Na, P. Shaojun, S. Tifeng, L. Feng, Z. Xiaobo et al., Molecular identification and culture trials of Eutreptiella gymnastica (Eutreptiales, Euglenophyceae), Chinese Journal of Oceanology and Limnology, vol.30, pp.446-455, 2012.

E. Nawrocki, D. Kolbe, and S. Eddy, Infernal 1.0: inference of RNA alignments, Bioinformatics, vol.25, issue.10, pp.1335-1337, 2009.
DOI : 10.1093/bioinformatics/btp157

F. Not, R. Siano, W. Kooistra, N. Simon, D. Vaulot et al., Diversity and Ecology of Eukaryotic Marine Phytoplankton, Advances in Botanical Research, vol.64, pp.1-53, 2012.
DOI : 10.1016/B978-0-12-391499-6.00001-3

M. Oborník, D. Modry, M. Luke?, E. Cernotikova-stribrna, and J. Cihlar, Morphology, Ultrastructure and Life Cycle of Vitrella brassicaformis n. sp., n. gen., a Novel Chromerid from the Great Barrier Reef, Protist, vol.163, issue.2, pp.306-323, 2012.
DOI : 10.1016/j.protis.2011.09.001

D. Oldenburg and A. Bendich, Changes in the Structure of DNA Molecules and the Amount of DNA Per Plastid During Chloroplast Development in Maize, Journal of Molecular Biology, vol.344, issue.5, pp.1311-1330, 2004.
DOI : 10.1016/j.jmb.2004.10.001

J. Paul, A. Alfreider, and B. Wawrik, Micro- and macrodiversity in rbcL sequences in ambient phytoplankton populations from the southeastern Gulf of Mexico, Marine Ecology Progress Series, vol.198, pp.9-18, 2000.
DOI : 10.3354/meps198009

J. Pawlowski, P. Esling, F. Lejzerowicz, T. Cedhagen, and T. Wilding, Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities, Molecular Ecology Resources, vol.30, issue.95, pp.1129-1140, 2014.
DOI : 10.1111/1755-0998.12261

J. Pawlowski, S. Audic, S. Adl, D. Bass, and L. Belbahri, CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms, PLoS Biology, vol.279, issue.(3), p.1001419, 2012.
DOI : 10.1371/journal.pbio.1001419.s002

URL : https://hal.archives-ouvertes.fr/hal-01258240

L. Pillet, D. Vargas, C. Pawlowski, and J. , Molecular Identification of Sequestered Diatom Chloroplasts and Kleptoplastidy in Foraminifera, Protist, vol.162, issue.3, pp.394-404, 2011.
DOI : 10.1016/j.protis.2010.10.001

J. Piñol, S. Andrés, V. Clare, E. Mir, G. Symondson et al., A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes, Molecular Ecology Resources, vol.7, issue.1, pp.18-26, 2014.
DOI : 10.1111/1755-0998.12156

F. Pompanon, B. Deagle, W. Symondson, D. Brown, S. Jarman et al., Who is eating what: diet assessment using next generation sequencing, Molecular Ecology, vol.7, issue.8, pp.1931-1950, 2012.
DOI : 10.1111/j.1365-294X.2011.05403.x

M. Price, P. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, p.9490, 2010.
DOI : 10.1371/journal.pone.0009490.s003

E. Pruesse, C. Quast, K. Knittel, B. Fuchs, W. Ludwig et al., SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Research, vol.35, issue.21, pp.7188-7196, 2007.
DOI : 10.1093/nar/gkm864

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, vol.41, issue.D1, pp.590-596, 2013.
DOI : 10.1093/nar/gks1219

T. Richardson and G. Jackson, Small Phytoplankton and Carbon Export from the Surface Ocean, Science, vol.315, issue.5813, pp.838-840, 2007.
DOI : 10.1126/science.1133471

A. Skovgaard, S. Karpov, and L. Guillou, The Parasitic Dinoflagellates Blastodinium spp. Inhabiting the Gut of Marine, Planktonic Copepods: Morphology, Ecology, and Unrecognized Species Diversity, Frontiers in Microbiology, vol.3, p.305, 2012.
DOI : 10.3389/fmicb.2012.00305

X. Shi, C. Lepère, D. Scanlan, and D. Vaulot, Plastid 16S rRNA Gene Diversity among Eukaryotic Picophytoplankton Sorted by Flow Cytometry from the South Pacific Ocean, PLoS ONE, vol.4, issue.4, p.18979, 2011.
DOI : 10.1371/journal.pone.0018979.s003

URL : https://hal.archives-ouvertes.fr/hal-00848706

R. Stern, A. Amorim, and E. Bresnan, Diversity and plastid types in Dinophysis acuminata complex (Dinophyceae) in Scottish waters, Harmful Algae, vol.39, pp.223-231, 2014.
DOI : 10.1016/j.hal.2014.07.013

T. Stoeck, D. Bass, M. Nebel, C. R. Jones, and M. , Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water, Molecular Ecology, vol.52, issue.2, pp.21-31, 2010.
DOI : 10.1111/j.1365-294X.2009.04480.x

URL : https://hal.archives-ouvertes.fr/hal-00497208

P. Taberlet, E. Coissac, F. Pompanon, C. Brochmann, and E. Willerslev, Towards next-generation biodiversity assessment using DNA metabarcoding, Molecular Ecology, vol.317, issue.8, pp.2045-2050, 2012.
DOI : 10.1111/j.1365-294X.2012.05470.x

F. Unrein, J. Gasol, F. Not, I. Forn, and R. Massana, Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters, The ISME Journal, vol.53, issue.1, pp.164-176, 2014.
DOI : 10.1078/0932-4739-00815

D. Vaulot, K. Romari, and F. Not, Are autotrophs less diverse than heterotrophs in marine picoplankton? Trends in Microbiology, pp.266-267, 2002.

D. Vaulot, C. Courties, and P. , A simple method to preserve oceanic phytoplankton for flow cytometric analyses, Cytometry, vol.67, issue.5, pp.629-635, 1989.
DOI : 10.1002/cyto.990100519

D. Vaulot, W. Eikrem, M. Viprey, and H. Moreau, The diversity of small eukaryotic phytoplankton (???3 ??m) in marine ecosystems, FEMS Microbiology Reviews, vol.32, issue.5, pp.795-820, 2008.
DOI : 10.1111/j.1574-6976.2008.00121.x

N. West, W. Schönhuber, N. Fuller, R. Amann, R. Rippka et al., Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides, Microbiology, vol.147, issue.7, pp.1731-1744, 2001.
DOI : 10.1099/00221287-147-7-1731

B. Williams and P. Keeling, Cryptic Organelles in Parasitic Protists and Fungi, Advances in Parasitology, vol.54, pp.9-67, 2003.
DOI : 10.1016/S0065-308X(03)54001-5

A. Worden, J. Nolan, and B. Palenik, Assessing the dynamics and ecology of marine picophytoplankton: The importance of the eukaryotic component, Limnology and Oceanography, vol.49, issue.1, pp.168-179, 2004.
DOI : 10.4319/lo.2004.49.1.0168

G. Zeidner, C. Preston, E. Delong, R. Massana, A. Post et al., Molecular diversity among marine picophytoplankton as revealed by psbA analyses, Environmental Microbiology, vol.51, issue.3, pp.212-216, 2003.
DOI : 10.1038/35088063

Z. Zhang, T. Cavalier-smith, and V. Green, Evolution of Dinoflagellate Unigenic Minicircles and the Partially Concerted Divergence of Their Putative Replicon Origins, Molecular Biology and Evolution, vol.19, issue.4, pp.489-500, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004104

F. Zhu, R. Massana, F. Not, M. D. Vaulot, and D. , Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene, FEMS Microbiology Ecology, vol.52, issue.1, pp.79-92, 2005.
DOI : 10.1016/j.femsec.2004.10.006

A. Zingone and T. Wyatt, Harmful algal blooms: keys to the understanding of the phytoplankton ecology, The Sea, pp.867-926, 2005.

M. Zubkov and G. Tarran, High bacterivory by the smallest phytoplankton in the North Atlantic Ocean, Nature, vol.69, issue.7210, pp.224-226, 2008.
DOI : 10.1038/nature07236