, GO:0071910:determination of liver left/right asymmetry, 0007165:signal transduction, 38, 99, 4e-05 GO:0005267:potassium channel activity, vol.6, pp.2-14
The globally distributed genus Alexandrium: multifaceted roles in marine ecosystems and impacts on human health, Harmful Algae, vol.14, pp.10-35, 2012. ,
Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management, Annual Review of Marine Science, vol.4, pp.143-176, 2012. ,
Habitat preference and the marine-speciation paradox, Proceedings of the Royal Society B-Biological Sciences, vol.270, pp.1399-1406, 2003. ,
Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea, Proceedings of the Royal Society B-Biological Sciences, vol.279, pp.129-138, 2011. ,
Limits to gene flow in a cosmopolitan marine planktonic diatom, Proceedings of the National Academy of Sciences, vol.107, pp.12952-12957, 2010. ,
An overview on the marine neurotoxin, saxitoxin: genetics, molecular targets, methods of detection and ecological functions, Marine Drugs, vol.11, pp.991-1018, 2013. ,
The variant call format and VCFtools, Bioinformatics, vol.27, pp.2156-2158, 2011. ,
Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum, Molecular Ecology, vol.23, pp.549-560, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01132961
Genome sequencing and population genomics in non-model organisms, Trends in Ecology & Evolution, vol.29, pp.51-63, 2014. ,
Hitchhiking under positive Darwinian selection, Genetics, vol.155, pp.1405-1413, 2000. ,
Evolution exacerbates the paradox of the plankton, Proceedings of the National Academy of Sciences, vol.105, pp.12365-12369, 2008. ,
Adaptive divergence in pigment composition promotes phytoplankton biodiversity, Nature, vol.432, pp.104-107, 2004. ,
Discovery of nuclear-encoded genes for the neurotoxin saxitoxin in dinoflagellates, PLoS ONE, vol.6, p.12, 2011. ,
European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation, Nature Communications, vol.5, p.5770, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01922671
Genomic islands of speciation in Anopheles gambiae, PLoS Biology, vol.3, pp.1572-1578, 2005. ,
Calcium channels in photosynthetic eukaryotes: implications for evolution of calcium-based signalling, New Phytologist, vol.187, pp.23-43, 2010. ,
Vertical niche partitioning between cryptic sibling species of a cosmopolitan marine planktonic protist, Molecular Ecology, vol.21, pp.4063-4073, 2012. ,
Dinoflagellate genome evolution, Annual Review of Microbiology, vol.65, pp.369-387, 2011. ,
Notes on Alexandrium population dynamics, Journal of Plankton Research, vol.19, pp.551-575, 1997. ,
A greedy algorithm for aligning DNA sequences, Journal of Computational Biology, vol.7, pp.203-214, 2000. ,
Spliced leader RNA trans-splicing in dinoflagellates, Proceedings of the National Academy of Sciences, vol.104, pp.4618-4623, 2007. ,
A new diatom species P. hallegraeffii sp. nov. 680 belonging to the toxic genus Pseudo-nitzschia (Bacillariophyceae) from the East 681 Australian Current, PLOS ONE, vol.13, p.195622, 2018. ,
Metatranscriptome analyses indicate resource 683 partitioning between diatoms in the field, Proc Natl Acad Sci, vol.112, pp.2182-90, 2015. ,
Nutrients in seawater using segmented flow analysis ,
, Practical Guidelines for the Analysis of Seawater, pp.143-78, 2009.
Transcriptional responses of three model 687 diatoms to nitrate limitation of growth, Front Mar Sci, vol.1, pp.1-15, 2014. ,
Gene expression studies for the analysis 689 of domoic acid production in the marine diatom Pseudo-nitzschia multiseries, BMC, vol.690 ,
, Mol Biol, vol.14, p.25, 2013.
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.692, pp.2114-2134, 2014. ,
Diatom Transcriptional and Physiological Responses 694 to Changes in Iron Bioavailability across Ocean Provinces. Front, vol.4, 2017. ,
Nutrient Limitation of Marine Photosynthesis. Primary 697 Productivity and Biogeochemical Cycles in the Sea, p.69, 1992. ,
The variant call format and VCFtools, Bioinformatics, vol.700, pp.2156-2164, 2011. ,
Transcriptome sequencing of three Pseudo-702 nitzschia species reveals comparable gene sets and the presence of Nitric Oxide 703 ,
, Synthase genes in diatoms. Sci Rep, vol.5, p.12329, 2015.
Do external resource ratios matter?, J Mar Syst, vol.3, issue.4, pp.170-80, 2010. ,
Haplotype-based variant detection from short-read sequencing, p.706 ,
, , 2012.
Algae in a phosphorus-limited landscape. In: Plaxton WC, Lambers 708 RNA-seq using the Trinity platform for reference generation and analysis, Nat Protoc, vol.711, pp.1494-512, 2013. ,
The Response of Diatom Central Carbon 713 ,
, Metabolism to Nitrogen Starvation Is Different from That of Green Algae and Higher 714
, Plant Physiol, vol.158, pp.299-312, 2012.
Media for the Culture of Oceanic 716 ,
, J Phycol, vol.2, pp.633-641, 1987.
Dynamics of Pseudo-nitzschia spp. and domoic acid 718 production in a macrotidal ecosystem of the Eastern English Channel, p.719 ,
URL : https://hal.archives-ouvertes.fr/hal-02433681
, Harmful Algae, vol.9, pp.218-244, 2010.
Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.721, pp.357-366, 2012. ,
Pseudo-nitzschia (Bacillariophyceae) species, domoic 723 acid and amnesic shellfish poisoning: revisiting previous paradigms, Phycologia, vol.724, pp.168-216, 2012. ,
Link between Domoic Acid Production and Cell Physiology 726 after Exchange of Bacterial Communities between Toxic Pseudo-nitzschia multiseries 727 and Non-Toxic Pseudo-nitzschia delicatissima, Mar Drugs, vol.12, pp.3587-607, 2014. ,
Inter and intra-specific growth and domoic acid 729 production in relation to nutrient ratios and concentrations in Pseudo-nitzschia: 730 phosphate an important factor, Harmful Algae, vol.64, pp.11-20, 2017. ,
Remodeling of intermediate metabolism in the 732 diatom Phaeodactylum tricornutum under nitrogen stress, Proc Natl Acad Sci, vol.733, pp.412-419, 2015. ,
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.735, pp.2078-2087, 2009. ,
Phosphorus physiological ecology and molecular mechanisms 737 in marine phytoplankton, J Phycol, vol.52, pp.10-36, 2016. ,
Moderated estimation of fold change and dispersion for RNA-739 seq data with DESeq2, Genome Biol, vol.15, p.550, 2014. ,
Digital expression profiling of novel diatom 741 transcripts provides insight into their biological functions, Genome Biol, vol.11, p.85, 2010. ,
Gene Expression Variation Resolves Species 743 and Individual Strains among Coral-Associated Dinoflagellates within the Genus 744 ,
, Genome Biol Evol, vol.8, pp.665-80, 2016.
The SILVA ribosomal RNA gene database project: 746 improved data processing and web-based tools, Nucleic Acids Res, vol.41, pp.590-596, 2013. ,
Life at the Leading Edge, Cell, vol.145, pp.1012-1034, 2011. ,
Thin layers and camouflage: hidden 749 ,
, spp. (Bacillariophyceae) populations in a fjord in the, vol.750
, Mar Ecol Prog Ser, vol.225, pp.123-160, 2002.
limma powers differential expression analyses for RNA-752 sequencing and microarray studies, Nucleic Acids Res, vol.43, pp.47-47, 2015. ,
Functions and mechanics of dynein motor proteins, Nat 754 Rev Mol Cell Biol, vol.14, pp.713-739, 2013. ,
Condensation of the isoprenoid and amino precursors in 756 the biosynthesis of domoic acid, Toxicon, vol.59, pp.25-33, 2012. ,
Model-based clustering for RNA-seq data, Bioinformatics, vol.758, pp.197-205, 2014. ,
Host-specific adaptation governs the interaction of 760 the marine diatom, Pseudo-nitzschia and their microbiota, ISME J, vol.8, pp.63-76, 2014. ,
Comparative analysis of diatom genomes reveals 762 substantial differences in the organization of carbon partitioning pathways, Algal Res, vol.763, pp.2-16, 2012. ,
Induction of domoic acid production in the toxic 765 diatom Pseudo-nitzschia seriata by calanoid copepods, Aquat Toxicol, vol.159, pp.52-61, 2015. ,
High diversity of Pseudo-nitzschia along the northern coast 767 of Sarawak (Malaysian Borneo), with descriptions of P. bipertita sp. nov. and P. limii 768 sp. nov. (Bacillariophyceae), J Phycol, vol.52, pp.973-89, 2016. ,
Intra-and interspecies differences in growth and 770 toxicity of Pseudo-nitzschia while using different nitrogen sources, This Issue, p.771 ,
, Contains Spec Sect Strains, vol.8, pp.792-810, 2009.
Nutrient ratios influence variability in Pseudo-773 nitzschia species diversity and particulate domoic acid production in the Bay of Seine 774 (France), Harmful Algae, vol.68, pp.192-205, 2017. ,
Pseudo-nitzschia physiological ecology, phylogeny, 776 toxicity, monitoring and impacts on ecosystem health, Harmful Algae--Requir, vol.777 ,
, Species-Specif Inf, vol.14, pp.271-300, 2012.
Underwater locomotion strategy by a benthic pennate diatom 779 Navicula sp, Protoplasma, vol.250, pp.1203-1215, 2013. ,
, Glutamine synthetase Gpd: glyceraldehyde 3-phosphate dehydrogenase Idh: Isocitrate dehydrogenase Il: Isocitrate lyase Mdh: Malate dehydrogenase Mpc: Mitochondrial phosphate carrier Ms: Malate synthase Nar:nitrate reductase Nir: nitrite reductase Nt: nitrate transporter Oct: Ornithine carbamoyltransferase Od:2-oxoglutarate dehydrogenase Pc: Pyruvate carboxylase Pdh: Pyruvate dehydrogenase Pec: Phosphoenolpyruvate carboxylase Pgk: Phospho-glycerate kinase Pgm: Phospho-glycerate mutase Pk: pyruvate kinase Ppc: Phosphoenolpyruvate carboxykinase Ppd: Pyruvate phosphate dikinase Ppt: PEP/PO4 3-translocator Rb:Rubisco Rbk: ribulokinase Rpe: ribulose phosphate epimerase Scs:Succinyl-CoA synthetase Sdpt: Sodium-dependent phosphate transport pn 2A Ss: Succinate synthase Tk, Aat: Aspartate aminotransferase Aco:Aconitase Ald: aldolase Arg:Arginase Asl: Arginosuccinate lyase Ass: Arginosuccinate synthase At: Ammonium transporter Bn: 5' bisphosphate nucleotidase Cs: Carbamoyl-P synthase Cs: Citrate synthase Eno: Enolase Fbp: fructose-1,6-bisphosphatase Fum: Fumarase Gad:Glutamate dehydrogenase Gas: Glutamate synthase Gis
Metatranscriptome of human faecal microbial communities in a cohort of adult men, Nature Microbiology, vol.3, issue.3, pp.356-366, 2018. ,
Impact of Natural Genetic Variation on Gene Expression Dynamics, PLoS Genetics, issue.6, p.9, 2013. ,
Promotion of cyst formation in the toxic dinoflagellate Alexandrium (Dinophyceae) by natural bacterial assemblages from Hiroshima Bay, Japan. Marine Ecology Progress Series, vol.191, pp.175-185, 1999. ,
Global biodiversity assessment and hyper-cryptic species complexes: more than one species of rlephant in the room?, Systematic Biology, vol.63, issue.4, pp.518-533, 2014. ,
Trans splicing of nuclear pre-mRNAs, Cell, issue.7, pp.1157-1160, 1990. ,
Deconstructing isolation-by-distance: The genomic consequences of limited dispersal, PLoS Genetics, vol.13, issue.8, pp.1-27, 2017. ,
Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the south african shrub protea repens, New Phytologist, vol.210, issue.1, pp.295-309, 2016. ,
Metatranscriptome analyses indicate resource partitioning between diatoms in the field, Proceedings of the National Academy of Sciences, vol.112, 2015. ,
Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean, Proceedings of the National Academy of Sciences, vol.112, pp.5972-5979, 2015. ,
Dosage automatique des nutriments dans les eaux marines : methodes en flux continu. . Institut francais de recherche pour l'exploitation de la mer, 2007. ,
Toxic Algal Blooms and Red tides: a Global Perspective, Biology, environmental science and toxicology, pp.11-16, 1989. ,
Physiology and bloom dynamics of toxic Alexandrium species, 1998. ,
The globally distributed genus Alexandrium: Multifaceted roles in marine ecosystems and impacts on human health, Harmful Algae, vol.14, pp.10-35, 2012. ,
Harmful algal blooms and eutrophication: Examining linkages from selected coastal regions of the United States, Harmful Algae, vol.8, issue.1, pp.39-53, 2008. ,
Long-Term Storage of Endocrine Tissues at -80°C Does Not Adversely Affect RNA Quality or Overall Histomorphology, Biopreservation and Biobanking, vol.11, issue.6, pp.366-370, 2013. ,
In situ life-cycle stages of Alexandrium fundyense during bloom development in Northport Harbor, Harmful Algae, vol.16, pp.20-26, 2012. ,
Genetic Assimilation and the Postcolonization Erosion of Phenotypic Plasticity in Island Tiger Snakes, Current Biology, vol.19, issue.22, pp.1932-1936, 2009. ,
The effects of frozen tissue storage conditions on the integrity of RNA and protein, vol.89, pp.518-528, 2014. ,
Dynamique sédimentaire de la marge continentale celtique (PhD dissertation), UNIVERSITE .DE· BORDEAUX, vol.1, 1981. ,
Potential contribution of the seed bank in coniferous plantations to the restoration of native deciduous forest vegetation, Acta Oecologica, vol.22, issue.2, pp.87-98, 2001. ,
Microbial community transcriptional networks are conserved in three domains at ocean basin scales, Proceedings of the National Academy of Sciences of the United States of America, vol.112, pp.5443-5448, 2015. ,
From stop to start: Tandem gene arrangement, copy number and Trans-splicing sites in the dinoflagellate Amphidinium carterae, PLoS ONE, issue.8, p.3, 2008. ,
Nuclear ribosomal dna internal transcribed spacer regions (its1 and its2) define discrete biogeographic groups in cladophora albida (chlorophyta) 1, Journal of Phycology, vol.28, issue.6, pp.839-845, 1992. ,
Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation, Proteomics, vol.15, issue.20, pp.3508-3520, 2015. ,
,
Novel initiation of RNA synthesis in vitro by vesicular stomatitis virus, Journal of virology, vol.255, issue.2, pp.37-40, 1975. ,
Influence of capping and polyadenylation on mRNA expression and on antisense RNA mediated inhibition of gene expression, Biochem Biophys Res Commun, issue.1, pp.97789-97794, 1997. ,
Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions, Environmental Microbiology, vol.13, issue.2, pp.340-349, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00604771
Distribution of Dinophysis spp. and Alexandrium minutum along French coasts since 1984 and their DSP and PSP toxicity levels, Toxic phytoplankton blooms in the sea, pp.469-474, 1993. ,
Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics, Frontiers in Marine Science, vol.5, pp.1-12, 2018. ,
Cryptic species as a window on diversity and conservation, Trends in Ecology and Evolution, vol.22, issue.3, pp.148-155, 2007. ,
Evidence for parasite-mediated selection during shortlasting toxic algal blooms, Proceedings of the Royal Society B: Biological Sciences, p.283, 1841. ,
URL : https://hal.archives-ouvertes.fr/hal-01400173
Characterization of Benthic Microbial Community Structure by High-Resolution Gas Chromatography of Fatty Acid Methyl Esters, Applied and Environmental Microbiology, vol.39, issue.6, pp.1212-1222, 1980. ,
Trimmomatic: A flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2120, 2014. ,
Sympatric Speciation: Models and Empirical Evidence, Evolution, and Systematics, vol.38, issue.1, pp.459-487, 2007. ,
Trans-splicing of pre-mRNA in plants, animals, and protists. Federation of, vol.7, pp.40-46, 1993. ,
Alexandrium catenella and Alexandrium minutum blooms in the Mediterranean Sea: Toward the identification of ecological niches, Harmful Algae, vol.7, issue.4, pp.515-522, 2008. ,
Rapid growth and concerted sexual transitions by a bloom of the harmful dinoflagellate Alexandrium fundyense (Dinophyceae), Limnology and Oceanography, vol.60, issue.6, pp.2059-2078, 2015. ,
Molecular Phylogenetics, 2002. ,
,
Expression divergence measured by transcriptome sequencing of four yeast species, BMC genomics, vol.12, issue.1, p.635, 2011. ,
Relative grazing impact of microzooplankton and mesozooplankton on a bloom of the toxic dinoflagellate Alexandrium minutum, Marine Ecology Progress Series, vol.259, pp.303-309, 2003. ,
Probing the evolution, ecology and physiology of marine protists using transcriptomics, Nature Reviews Microbiology, vol.15, issue.1, pp.6-20, 2017. ,
Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea, Proceedings of the Royal Society B: Biological Sciences, vol.279, pp.129-138, 1726. ,
Chemical ecology of eukaryotic microalgae in marine ecosystems, Phycologia, vol.42, issue.4, pp.420-447, 2003. ,
Control of toxic marine dinoflagellate blooms by serial parasitic killers, Science, vol.322, issue.5905, pp.1254-1257, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02409729
Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3, Nucleic Acids Research, vol.35, issue.8, pp.2573-2583, 2007. ,
Toxin production of Alexandrium minutum (Dinophyceae) from the Bay of Plenty, Toxicon, vol.35, issue.3, pp.168-175, 1997. ,
Immunofluorescent detection of a PSPproducing dinoflagellate, <i>Alexandrium minutum</i> , from Bay of Plenty, New Zealand Journal of Marine and Freshwater Research, vol.33, issue.4, pp.533-543, 1999. ,
Étude sur la prolifération de la micro algue Alexandrium minutum en rade de Brest, p.61, 2014. ,
The Bay of Brest (France), a new risky site for toxic Alexandrium minutum blooms and PSP shellfish contamination, Harmful Algae News, vol.51, issue.51, pp.4-5, 2015. ,
The Bay of Brest (France), a new risky site for toxic Alexandrium minutum blooms and PSP shellfish contamination, Harmful Algae News, vol.51, issue.51, pp.4-5, 2015. ,
Long-term variation of the Bay of Brest ecosystem: Benthic-pelagic coupling revisited, Marine Ecology Progress Series, pp.35-48, 0200. ,
URL : https://hal.archives-ouvertes.fr/hal-00524757
, , 2010.
, De Novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits, PLoS ONE, issue.12, p.5
, , 1997.
, Hydrothermal-vent alvinellid polychaete dispersal in the eastern Pacific. Limnology and Oceanography, vol.42, pp.67-80
Insights into the loss factors of phytoplankton blooms: The role of cell mortality in the decline of two inshore alexandrium blooms, Limnology and Oceanography, vol.62, issue.4, pp.1742-1753, 2017. ,
Morphology and molecular phylogeny of Prorocentrum consutum SP. Nov. (dinophyceae), a new benthic dinoflagellate from South Brittany (northwestern France), Journal of Phycology, vol.46, issue.1, pp.183-194, 2010. ,
Dispersal similarly shapes both population genetics and community patterns in the marine realm, Scientific Reports, p.6, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01444635
Diatom Transcriptional and Physiological Responses to Changes in Iron Bioavailability across Ocean Provinces, Frontiers in Marine Science, p.4, 2017. ,
, Cryptic Species and Ancient Separations in a Globally Distributed Shorefish, vol.55, pp.807-820, 2007.
A survey of best practices for RNA-seq data analysis, Genome Biology, vol.17, issue.1, pp.1-19, 2016. ,
Mechanisms of succession in natural communities and their role in community stability and organization, The American Naturalist, vol.111, issue.982, pp.1119-1144, 1977. ,
Transcriptome dynamics of Arabidopsis REFERENCES during sequential biotic and abiotic stresses. The Plant journal : for cell and molecular biology, vol.86, pp.249-267, 2016. ,
The influence of bloom intensity on the encystment rate and persistence of alexandrium minutum in cork harbor, ireland. Harmful algae, vol.31, pp.114-124, 2014. ,
Larval dispersal and marine population connectivity. Annual review of marine science, vol.1, pp.443-66, 2009. ,
Population Connectivity in Marine Systems: An Overview, Oceanography, vol.20, issue.3, pp.14-21, 2007. ,
, Speciation. Sinauer.Com, 2004.
Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents, Heliyon, vol.3, issue.10, 2017. ,
Cryptic species revealed by molecular phylogenetic analysis of sequences obtained from basidiomata of <i>Tulasnella</i>, Mycologia, vol.106, issue.4, pp.708-722, 2014. ,
Behavior, physiology and the niche of depthregulating phytoplankton, Nato Asi Series G Ecological Sciences, vol.41, pp.559-580, 1978. ,
Evaluating population connectivity for species of conservation concern in the American Great Plains, Biodiversity and Conservation, vol.22, issue.11, pp.2583-2605, 2013. ,
An overview on the marine neurotoxin, saxitoxin: Genetics, moleculartargets, methods of detection and ecological functions, Marine Drugs, vol.11, issue.4, pp.991-1018, 2013. ,
On the origin of species by means of natural selection, 1859. ,
Algal Taxonomy: A Road to Nowhere?, Journal of Phycology, vol.49, issue.2, pp.215-225, 2013. ,
Temperature and salinity induce differential responses in life histories of cryptic nematode species, Journal of Experimental Marine Biology and Ecology, vol.472, pp.54-62, 2015. ,
,
Community Genomics among microbial assemblages in the Ocean' s Interior, Science, pp.496-503, 2006. ,
Divergence in gene regulation contributes to sympatric speciation of Shewanella baltica strains, Applied and Environmental Microbiology, vol.84, issue.4, 2018. ,
Ernst Mayr and the modern concept of species. Proceedings of the National Academy of Sciences, vol.102, pp.6600-6607, 2005. ,
Delineation of two sibling red algal species, gracilaria gracilis and gracilaria dura (gracilariales, rhodophyta), using multiple dna markers: Resurrection of the species g. dura previously described in the northern atlantic 200 years ago, Journal of Phycology, vol.46, issue.4, pp.720-727, 2010. ,
Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum, Molecular Ecology, vol.23, issue.3, pp.549-560, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01132961
Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans, Molecular Ecology, vol.21, issue.10, pp.2519-2533, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01000602
Genetics and the orign of species, 1937. ,
Chromosome structure in the dinoflagellates and the problem of mesokaryotic cells, International Congress Series, vol.97, pp.339-345, 1965. ,
The <b>ade4</b> Package: Implementing the Duality Diagram for Ecologists, Journal of Statistical Software, vol.22, issue.4, pp.1-20, 2007. ,
Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank -Evaluation of RNA quality and stability, BMC Research Notes, vol.7, issue.1, pp.1-10, 2014. ,
The Effects of UV-B Radiation on Dinoflagellates, Journal of Plant Physiology, vol.138, issue.3, pp.80287-80294, 1991. ,
Exotic flagellates of coastal North Sea waters, Helgol. Wiss. Meeresunters, vol.52, issue.3-4, pp.235-242, 1998. ,
Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing, BMC Genomics, vol.7, issue.1, 2006. ,
Diversity and dynamics of a widespread bloom of the toxic dinoflagellate Alexandrium fundyense, PLoS ONE, vol.6, issue.7, pp.1-8, 2011. ,
An efficient method for long-term room temperature storage of RNA, European Journal of Human Genetics, vol.22, issue.3, pp.379-385, 2014. ,
Perception of environmental signals by a marine diatom, Science, issue.5475, pp.2363-2369, 2000. ,
The Microbial Engines That REFERENCES Drive Earth 's Biogeochemical Cycles, Science, vol.320, issue.5879, pp.1034-1039, 2008. ,
Evaluating the role of natural selection in the evolution of gene regulation, Heredity, vol.100, issue.2, pp.191-199, 2008. ,
Microbial biomass, activity, and community structure in subsurface soils, Groundwater, vol.24, issue.3, pp.365-374, 1986. ,
The hidden sexuality of Alexandrium minutum: An example of overlooked sex in dinoflagellates, PLoS ONE, vol.10, issue.11, pp.1-21, 2015. ,
Comparative study of the life cycles of Alexandrium tamutum and Alexandrium minutum (Gonyaulacales, Dinophyceae) in culture, Journal of Phycology, vol.43, issue.5, pp.1039-1053, 2007. ,
, , 2008.
Host-specificity, and Strain Selectivity of the Dinoflagellate Parasite Parvilucifera sinerae sp. nov. (Perkinsozoa) ,
, Protist, vol.159, issue.4, pp.563-578
Interactive effects of salinity and temperature on planozygote and cyst formation of alexandrium minutum (dinophyceae) in culture 1, Journal of phycology, vol.47, issue.1, pp.13-24, 2011. ,
Cryptic species as a window into the paradigm shift of the species concept, Molecular Ecology, vol.27, issue.3, pp.613-635, 2018. ,
Molecular and morphological data reveal three new cryptic species of <i>Chiasmocleis</i> (Mehely 1904) (Anura, Microhylidae) endemic to the Atlantic Forest, Brazil. PeerJ, issue.5, 1904. ,
The effects of genetic variation on gene expression dynamics during development, Nature, issue.7482, pp.208-211, 2014. ,
Toxin profiles of natural populations and cultures ofAlexandrium minutum Halim from Galician (Spain) coastal waters, Journal of Applied Phycology, vol.6, issue.3, pp.275-279, 1994. ,
Toxin production and competitive abilities under phosphorus limitation of Alexandrium species, Harmful Algae, vol.3, issue.2, pp.131-139, 2004. ,
Gene expression drives local adaptation in humans Gene expression drives local adaptation in humans, pp.1089-1096, 2013. ,
Evidence for widespread adaptive evolution of gene expression in budding yeast, Proceedings of the National Academy of Sciences, vol.107, issue.7, pp.2977-2982, 2010. ,
Microbial community gene expression in ocean surface waters, Proceedings of the National Academy of Sciences of the United States of America, vol.105, pp.3805-3810, 2008. ,
CD-HIT: Accelerated for clustering the next-generation sequencing data, Bioinformatics, vol.28, issue.23, pp.3150-3152, 2012. ,
Long-term competitive dynamics of two cryptic rotifer species: Diapause and fluctuating conditions, PLoS ONE, vol.10, issue.4, pp.1-13, 2015. ,
Relationship between vegetative cells and cyst production during Alexandrium minutum bloom in Arenys de Mar harbour (NW Mediterranean), Journal of Plankton Research, vol.26, issue.6, pp.637-645, 2004. ,
Molecular evidence for the coexistence of two sibling species in Pylaiella littoralis (Ectocarpales, Phaeophyceae) along the Brittany coast, Journal of Phycology, vol.51, issue.3, pp.480-489, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01147191
Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature, vol.525, issue.7569, pp.372-375, 2015. ,
First report of Alexandrium minutum Halim in a Mediterranean lagoon, Cryptogamie Algol, vol.15, pp.47-52, 1994. ,
Environmental factors and seasonal occurrence of the dinoflagellate Alexandrium minutum, a PSP potential producer, in a Mediterranean lagoon, Estuarine, Coastal and Shelf Science, vol.42, issue.5, pp.539-549, 1996. ,
Natural selection on gene expression, Trends in Genetics, vol.22, issue.8, pp.456-461, 2006. ,
The Geography of Marine Larval Dispersal : Coupling Genetics with Fine-Scale Physical Oceanography Published by : Ecological Society of America THE GEOGRAPHY OF MARINE LARVAL DISPER-SAL : COUPLING GENETICS WITH FINE-SCALE PHYSICAL OCEANOG-RAPHY, Ecology, vol.84, issue.11, pp.2989-2998, 2003. ,
Eukaryotic phytoplankton community spatiotemporal dynamics as identified through gene expression within a eutrophic estuary, Journal Article]. Environmental Microbiology, vol.11, issue.5, pp.1095-1111, 2011. ,
The role of calcium in the chlamydomonas-reinhardtii mating reaction, Journal of Cell Biology, vol.121, issue.2, pp.365-374, 1993. ,
OCEANOGRAPHY : METHODS Effects of preservation and storage of microcrustaceans in RNA later on RNA and DNA degradation, LIMNOLOGY and OCEANOGRAPHY: METHODS, vol.3, pp.143-148, 2005. ,
,
Metatranscriptomic approach to REFERENCES analyze the functional human gut microbiota, PLoS ONE, vol.6, issue.3, pp.1-9, 2011. ,
Re-occurrence of red tide in Cork Harbor, 1989. ,
Effects of salinity and two coastal waters on the growth and toxin content of the dinoflagellate Alexandrium minutum, Journal of Plankton Research, vol.25, issue.10, pp.1185-1199, 2003. ,
Global and local factors driving the phenology of Alexandrium minutum (Halim) blooms and its toxicity, Harmful Algae, vol.67, pp.44-60, 2017. ,
Gut flora in health and disease, Lancet, vol.361, issue.9356, pp.512-519, 2003. ,
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, pp.597-604, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01253994
Algaebase. world-wide electronic publication, national university of ireland, 2014. ,
Ecological advantages of toxin production by the dinoflagellate Alexandrium minutum under phosphorus limitation, Marine Ecology Progress Series, vol.225, pp.169-176, 2002. ,
Correlation between Protein and mRNA Abundance in Yeast, Molecular and Cellular Biology, vol.19, issue.3, pp.1720-1730, 1999. ,
Insights into a dinoflagellate genome through expressed sequence tag analysis, BMC Genomics, vol.6, pp.1-13, 2005. ,
Coccolithophore assemblages and morphotypes of Emiliania huxleyi in the boundary zone between the cold Oyashio and warm Kuroshio currents off the coast of Japan. Marine Micropaleontology, vol.55, pp.19-47, 2005. ,
Alexandrium minutum n. gen. n. sp., dinoagelle provocant des eaux rouges, Vie et Milieu, vol.11, pp.102-105, 1960. ,
Species of the Toxigenic Dinoflagellate Genus Alexandrium in Southeastern Australian Waters, Botanica Marina, vol.34, issue.6, pp.575-588, 1991. ,
Monomethylated cap structures facilitate RNA export from the nucleus, Cell, vol.63, issue.1, pp.109-118, 1990. ,
Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis, Scientific Reports, vol.7, pp.1-14, 2017. ,
Morphology, toxin composition and LSU rDNA phylogeny of Alexandrium minutum (Dinophyceae) from, 2003. ,
, Rhodopsin-regulated calcium currents in Chlamydomonas, vol.2, pp.317-335, 1991.
Genetic connectivity and inter-population seed dispersal of Banksia hookeriana at the landscape scale, Annals of Botany, vol.106, issue.3, pp.457-466, 2010. ,
Transgenerational epigenetic inheritance: myths and mechanisms, Cell, vol.157, issue.1, pp.95-109, 2014. ,
, Genetic Approaches to Measuring Connectivity. Oceanography, vol.20, pp.70-79, 2007.
,
In Vitro -In Vivo Correlation of Gene Expression Alterations Induced by Liver Carcinogens, Current Medicinal Chemistry, vol.19, issue.11, pp.1721-1730, 2012. ,
Environmental controls on Emiliania huxleyi morphotypes in the Benguela coastal upwelling system (SE Atlantic), Marine Ecology Progress Series, vol.448, pp.51-66, 2012. ,
Condition Dependence and Adaptation-by-Time: Breeding Date, Life History, and Energy Allocation within a Population of Salmon, Oikos, vol.85, issue.3, p.499, 1999. ,
Population transcriptomics in Daphnia: The role of thermal selection, Molecular Ecology, vol.27, issue.2, pp.387-402, 2018. ,
,
Metatranscriptomic analyses of plankton communities inhabiting surface and subpycnocline waters of the chesapeake bay during oxic-anoxic-oxic transitions, Applied and environmental microbiology, vol.80, issue.1, pp.328-338, 2014. ,
Measuring genetic differentiation from pool-seq data, p.282400, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01936905
The nature of rhodopsin-triggered photocurrents in Chlamydomonas, 1996. ,
Kinetics and influence of divalent ions, Biophysical Journal, vol.70, issue.2, pp.924-931 ,
Can a seed bank maintain the genetic variation in the above ground plant population?, vol.117, pp.1-5, 2008. ,
The remarkable chloroplast genome of dinoflagellates, Journal of Experimental Botany, vol.59, issue.5, pp.1035-1045, 2008. ,
,
Shifting metabolic priorities among key protistan taxa within and below the euphotic zone, Environmental Microbiology, vol.00, pp.1-15, 2018. ,
Maturation of polycistronic pre-mRNA in Trypanosoma brucei: analysis of trans splicing and poly(A) addition at nascent RNA transcripts from the hsp70 locus, Molecular and cellular biology, vol.11, issue.6, pp.3180-3190, 1991. ,
Concluding Remarks, Cold Spring Harbor Symposia on Quantitative Biology, issue.22, pp.415-427, 1957. ,
The Paradox of the Plankton, The American Naturalist, vol.106, issue.948, pp.254-257, 1961. ,
Influence of environmental and nutritional factors on growth, toxicity, and toxin profile of dinoflagellate Alexandrium minutum, Toxicon, vol.38, issue.11, pp.1491-1503, 2000. ,
Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria, BMC Biology, vol.5, pp.1-17, 2007. ,
Microarray experiments and factors which affect their reliability, Biology Direct, vol.10, issue.1, pp.1-14, 2015. ,
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiomespecific functionality. Microbiome, vol.4, pp.1-18, 2016. ,
Global distribution of microbial abundance and biomass in subseafloor sediment, Proceedings of the National Academy of Sciences, vol.109, pp.16213-16216, 2012. ,
Conceptual issues in local adaptation, Ecology Letters, vol.7, issue.12, pp.1225-1241, 2004. ,
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing, PLoS Biology, issue.6, p.12, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01109521
Marine Protists Are Not Just Big Bacteria, Current Biology, vol.27, issue.11, pp.541-549, 2017. ,
Phenotypic plasticity: molecular mechanisms and adaptive significance, Compr Physiol, vol.2, issue.2, pp.1417-1456, 2012. ,
Heterogeneous distribution in sediments and dispersal in waters of Alexandrium minutum in a semi-enclosed coastal ecosystem, Harmful Algae, vol.60, pp.81-91, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01408984
In vitro and in vivo culture effects on mRNA expression of genes involved in metabolism and apoptosis in bovine embryos, Reproduction, fertility, and development, vol.17, pp.775-784, 2005. ,
Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes, ISME Journal, vol.10, issue.8, pp.1877-1890, 2016. ,
Dinoflagellate chloroplasts -Where have all the genes gone?, Trends in Genetics, vol.20, issue.5, pp.261-267, 2004. ,
Checklist of phytoplank-ton in the Skagerrak-Kattegat, 2000. ,
, Wind and temperature controls on Alexandrium blooms, vol.28, pp.31-36, 2000.
Competition for phosphorus between two dinoflagellates: A toxic Alexandrium minutum and a non-toxic Heterocapsa triquetra, Journal of Experimental Marine Biology and Ecology, vol.358, issue.2, pp.124-135, 2008. ,
Trans splicing in trypanosomes -archaism or adaptation?, Trends in Genetics, vol.5, issue.C, pp.90082-90088, 1989. ,
Symbiodinium (Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates, Journal of Phycology, vol.41, issue.4, pp.880-886, 2005. ,
Cryptic or pseudocryptic: Can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex, Ecology and Evolution, vol.5, issue.12, pp.2374-2385, 2015. ,
cAMP in the cell cycle of the dinoflagellate <i>Crypthecodinium cohnii</i> (Dinophyta), Journal of Phycology, vol.37, pp.79-85, 2001. ,
WGCNA: An R package for weighted correlation network analysis, BMC Bioinformatics, p.9, 2008. ,
Fast gapped-read alignment with bowtie 2, Nature methods, vol.9, issue.4, p.357, 2012. ,
Présence d'un protogonyaulax sp. sur le littoral atlantique français pendant l'hiver 1987, Cryptogamie Algologie, vol.9, issue.4, pp.273-278, 1988. ,
Morphological and genetic characterization of benthic dinoflagellates of the genera coolia, ostreopsis and prorocentrum from the south-eastern bay of biscay, European Journal of Phycology, vol.46, issue.1, pp.45-65, 2011. ,
Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding, Environmental Microbiology, vol.18, issue.2, pp.609-626, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01305586
Fungal diversity in deep-sea hydrothermal ecosystems. Applied and Environmental Microbiology, vol.75, pp.6415-6421, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00429860
,
Evolutionary processes and cellular functions underlying divergence in Alexandrium minutum, Molecular ecology, issue.20, p.25, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01400194
Genetic diversity within and genetic differentiation between blooms of a microalgal species, Environmental Microbiology, vol.14, issue.9, pp.2395-2404, 2012. ,
Use of HPLC for toxin analysis of shellfish contaminated by an Alexandrium minutum strain, Toxic phytoplankton blooms in the sea, pp.413-418, 1993. ,
Factors affecting outbreaks of high-density Cochlodinium polykrikoides red tides in the coastal seawaters around Yeosu and Tongyeong, Korea. Marine Pollution Bulletin, vol.52, issue.10, pp.1249-1259, 2006. ,
The sva package for removing batch effects and other unwanted variation in high-throughput experiments, Bioinformatics, issue.6, pp.882-885, 2012. ,
Plankton and nutrient dynamics in marine waters, Ophelia, vol.41, issue.1, pp.153-172, 1995. ,
Differential Responses of the Coral Host and Their Algal Symbiont to Thermal Stress, PLoS ONE, vol.6, issue.10, 2011. ,
Dispersion/dilution enhances phytoplankton blooms in low-nutrient waters, Nature Communications, vol.8, p.14868, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01502211
Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach, Deep-Sea Research Part II: Topical Studies in Oceanography, vol.214, pp.86-87, 2013. ,
DNA-based species delimitation in algae, European Journal of Phycology, vol.49, issue.2, pp.179-196, 2014. ,
,
Linking in vitro vs in situ gene expression variations to genetic background : investigating species divergence under the molecular physiology scope, FEMS Microbiology Ecology, 2018. ,
A Lagrangian tool for modelling ichthyoplankton dynamics, Environmental Modelling and Software, vol.23, issue.9, pp.1210-1214, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00405768
Rare earth tagging methods for the study of larval dispersal by marine invertebrates, Limnology and Oceanography, vol.38, pp.346-360, 1993. ,
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009. ,
, , 2009.
, The Sequence Alignment/Map format and SAMtools, vol.25, pp.2078-2079
Genetic evidence for male-biased dispersal in the Siberian jay (Perisoreus infaustus) based on autosomal and Z-chromosomal markers, Molecular Ecology, vol.19, issue.23, pp.5281-5295, 2010. ,
Spliced leader RNA-mediated trans-splicing in a dinoflagellate, Karenia brevis, Journal of Eukaryotic Microbiology, vol.54, issue.5, pp.427-435, 2007. ,
Identifying biochemical phenotypic differences between cryptic species, Biology Letters, vol.10, issue.9, pp.20140615-20140615, 2014. ,
Phylogeny, biogeography, and species boundaries within the Alexandrium minutum group, Harmful Algae, vol.4, issue.6, pp.1004-1020, 2005. ,
Species boundaries and global biogeography of the alexandrium tamarense complex (dinophyceae) 1, Journal of Phycology, vol.43, issue.6, pp.1329-1338, 2007. ,
Effect of salinity on growth and toxin production of Alexandrium minutum isolated from a shrimp culture pond in northern Vietnam, Journal of Applied Phycology, vol.23, issue.5, pp.857-864, 2011. ,
Effects of light and temperature on growth, nitrate uptake, and toxin production of two tropical dinoflagellates: Alexandrium tamiyavanichii and Alexandrium minutum (Dinophyceae), Journal of Phycology, vol.42, issue.4, pp.786-799, 2006. ,
Genomic understanding of dinoflagellates, Research in Microbiology, vol.162, issue.6, pp.551-569, 2011. ,
High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob genes for dinoflagellate DNA barcoding, Applied and Environmental Microbiology, vol.75, issue.5, pp.1279-1290, 2009. ,
Comparison of gene expression during in vivo and in vitro postnatal retina development, J Ocul Biol Dis Infor, vol.1, issue.2-4, pp.59-72, 2008. ,
On the Dependency of Cellular Protein Levels on mRNA Abundance, Cell, vol.165, issue.3, pp.535-550, 2016. ,
Scaling laws predict global microbial diversity, Proceedings of the National Academy of Sciences, vol.113, issue.21, pp.5970-5975, 2016. ,
,
SNP calling from RNA-seq data without a reference genome: Identification, quantification, differential analysis and impact on the protein sequence, Nucleic Acids Research, vol.44, issue.19, pp.1-13, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01352586
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, vol.15, issue.12, pp.1-21, 2014. ,
Cryptic and pseudo-cryptic diversity in diatoms-with descriptions of pseudo-nitzschia hasleana SP, NOV. AND P. Fryxelliana SP. NOV. Journal of Phycology, vol.48, issue.2, pp.436-454, 2012. ,
Cell morphology and PSP-toxin profiles of Alexandrium minutum in the Marlborough Sounds, New Zealand Journal of Marine and Freshwater Research, vol.31, issue.3, pp.403-409, 1997. ,
Evidence for isolation by time in the European eel (Anguilla anguilla L.), Molecular Ecology, vol.15, issue.8, pp.2095-2107, 2006. ,
Nitrogen and phosphorus requirements of an Alexandrium minutum bloom in the Penzé estuary, France. Limnology and Oceanography, vol.49, issue.4, pp.1108-1114, 2004. ,
,
Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests, Nature Ecology and Evolution, vol.1, issue.4, pp.1-8, 2017. ,
Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ, 3, e1420, 2015. ,
De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease, Genetica, vol.143, issue.2, pp.225-239, 2015. ,
Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability, Proceedings of the National Academy of Sciences of the United States of America, vol.109, 2012. ,
Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries, Scientific Reports, vol.6, pp.1-10, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01436790
Rna-seq: an assessment of technical reproducibility and comparison with gene expression arrays, Genome research, 2008. ,
Bacterial induction of temporary cyst formation by the dinoflagellate Lingulodinium polyedrum, Aquatic Microbial Ecology, vol.50, issue.1, pp.51-62, 2007. ,
A hierarchy of species concepts: the denouement in the saga of the species problem. Species. The units of biodiversity, pp.85758-85766, 1997. ,
Systematics and the Origin of Species, 1942. ,
Animal Species and Evolution, 1963. ,
Plankton distribution and ocean dispersal, Journal of Experimental Biology, vol.215, issue.6, pp.1008-1016, 2012. ,
Biodiversity of harmful marine algae, 2013. ,
A study of TP53 RNA splicing illustrates pitfalls of RNA-seq methodology, Cancer Research, vol.76, issue.24, pp.7151-7159, 2016. ,
Challenging microorganisms surveys in situ : new highlights into the gene expression dynamics of a marine phytoplankton, Molecular Ecology, 2018. ,
Inter and intra specific transcriptional and phenotypic responses of Pseudo-nitzchia under different nutrient conditions, Molecular Ecology, 2018. ,
Fine scale ednemism o coral reefs: Archipelagic differentiation in turbid gastropods, Evolution, vol.59, issue.1, pp.113-125, 2005. ,
Genetic differentiation, isolation-by-distance, and metapopulation dynamics of the Arizona treefrog (Hyla wrightorum) in an isolated portion of its range, PLoS ONE, vol.11, issue.8, pp.1-23, 2016. ,
Quantifying connectivity in the coastal ocean with application to the Southern California Bight, Journal of Geophysical Research: Oceans, vol.114, issue.10, pp.1-21, 2009. ,
,
Genetic inheritance of gene expression in human cell lines, American journal of human genetics, vol.75, issue.6, pp.1094-1105, 2004. ,
Species delimitation and phylogeographic analyses in the Ectocarpus subgroup siliculosi (Ectocarpales, Phaeophyceae), Journal of Phycology, vol.53, issue.1, pp.17-31, 2017. ,
Three Alexandrium species from coastal Tyrrhenian waters, Toxic marine phytoplankton, pp.82-87, 1990. ,
Sizing up metatranscriptomics, ISME Journal, vol.7, issue.2, pp.237-243, 2013. ,
Surface ocean metabarcoding confirms limited diversity in REFERENCES planktonic foraminifera but reveals unknown hyper-abundant lineages, Scientific Reports, vol.8, issue.1, pp.1-10, 2018. ,
Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: The amazing dinoflagellates, European Journal of Cell Biology, vol.84, issue.2-3, pp.137-149, 2005. ,
Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence, PLoS ONE, vol.5, issue.3, 2010. ,
Diversity and distribution of tintinnids in chilika lagoon with description of new records, Indian Journal of Fisheries, issue.1, p.62, 2015. ,
Condensing the omics fog of microbial communities, Trends in Microbiology, vol.21, issue.7, pp.325-333, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02329342
Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: Evidence for Trans splicing, Cell, vol.47, issue.4, pp.90616-90617, 1986. ,
Genetic diversity, morphological uniformity and polyketide production in dinoflagellates (amphidinium, dinoflagellata), PLoS ONE, vol.7, issue.6, pp.1-14, 2012. ,
Searching for a needle in a stack of needles: Challenges in metaproteomics data analysis, Molecular BioSystems, vol.9, issue.4, pp.578-585, 2013. ,
Ecological equivalence of species within phytoplankton functional groups, Functional Ecology, vol.30, issue.10, p.000385511500011, 2016. ,
Microsatellite markers reveal population genetic structure of the toxic dinoflagellate alexandrium tamarense (dinophyceae) in japanese coastal waters 1, Journal of Phycology, vol.43, issue.1, pp.43-54, 2007. ,
Organization of the mitochondrial genome in the dinoflagellate Amphidinium carterae, Molecular Biology and Evolution, vol.24, issue.7, pp.1528-1536, 2007. ,
Local Ion Currents Controlling the Localized Cytoplasmic Movement Associated with Feeding Initiation of Noctiluca. Protoplasma, vol.137, pp.125-133, 1987. ,
Non-indigenous phytoplankton species in the North Sea: supposed region of origin and possible transport vector. Archive of Fishery and Marine Research, vol.46, pp.181-194, 1998. ,
Seasonality in the excystment of Alexandrium minutum and Alexandrium tamarense in Irish coastal waters, Harmful Algae, vol.10, issue.6, pp.629-635, 2011. ,
An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA, Nucleic Acids Research, vol.19, issue.2, pp.227-235, 1991. ,
Adaptive Evolution of Gene Expression in Drosophila, Cell Reports, vol.20, issue.6, pp.1385-1395, 2017. ,
Modification of voltage-sensitive inactivation of Na+ current by external Ca2+ in the marine dinoflagellate Noctiluca miliaris, Journal of Comparative Physiology A, vol.176, issue.5, pp.635-640, 1995. ,
Novel dinoflagellate clock-related genes identified through microarray analysis, Journal of Phycology, vol.39, issue.3, pp.519-526, 2003. ,
Cryptic diversity in vertebrates: Molecular data double estimates of species diversity in a radiation of Australian lizards (Diplodactylus, Gekkota). Proceedings of the, Royal Society B: Biological Sciences, vol.276, pp.2001-2007, 1664. ,
Biobanking Practice: RNA Storage at Low Concentration Affects Integrity, Biopreservation and Biobanking, vol.12, issue.1, pp.46-52, 2014. ,
Transcript length bias in RNA-seq data confounds systems biology, Biology Direct, vol.4, pp.1-10, 2009. ,
Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton, 2011. ,
, Isme Journal, vol.5, issue.12, pp.1881-1895
Pattern and synchrony of gene expression among sympatric marine microbial populations, Proceedings of the National Academy of Sciences, vol.110, issue.6, pp.488-497, 2013. ,
,
Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages, Science, vol.345, issue.6193, pp.207-212, 2014. ,
The Genetic and Mechanistic Basis for Variation in Gene Regulation, PLoS Genetics, issue.1, p.11, 2015. ,
Transcriptome sequencing in an ecologically important tree species: Assembly, annotation, and marker discovery, BMC Genomics, issue.1, p.11, 2010. ,
Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium, Genome biology and evolution, vol.8, issue.3, pp.665-680, 2016. ,
Extensive cryptic species diversity and fine-scale endemism in the marine red alga <i>Portieria</i> in the Philippines, Proceedings of the Royal Society B: Biological Sciences, p.280, 1753. ,
Organisms and responses to environmental change, Marine Genomics, vol.4, issue.4, pp.237-243, 2011. ,
,
Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex, Journal of Phycology, vol.52, issue.2, pp.184-199, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01288747
Large variability of bathypelagic microbial eukaryotic communities across the world's oceans, ISME Journal, vol.10, issue.4, pp.945-958, 2016. ,
Probable origin and toxin profile of Alexandrium tamarense (Lebour) Balech from southern Brazil, Harmful Algae, vol.5, issue.1, pp.36-44, 2006. ,
Dinoflagellate Cysts in Recent Sediments from the West Coast of Sweden, Offprint Botanica Marina, vol.43, pp.69-79, 2000. ,
Genome evolution across 1,011 saccharomyces cerevisiae isolates, others, vol.556, p.339, 2018. ,
URL : https://hal.archives-ouvertes.fr/cea-01872910
Perspective: Genetic Assimilation and a Possible Evolutionary Paradox: Can Macroevolution Sometimes Be So Fast As To Pass Us By? Evolution, vol.57, p.1455, 2003. ,
Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex, Biological Journal of the Linnean Society, pp.23-38, 2004. ,
Larval Transport and Dispersal in the Coastal Ocean and Consequences for Population Connectivity, Oceanography, vol.20, issue.3, pp.22-39, 2007. ,
Analysis of microbial gene transcripts in environmental samples, Applied and Environmental Microbiology, vol.71, issue.7, pp.4121-4126, 2005. ,
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre, Environmental Microbiology, vol.11, issue.6, pp.1358-1375, 2009. ,
MRNA splicing in trypanosomes, International Journal of Medical Microbiology, vol.302, issue.4-5, pp.221-224, 2012. ,
Sexual reproduction and ecophysiology of the marine dinoflagellate Alexandrium minutum Halim, 1999. ,
Ecosystem processes and interactions in a morass of diversity, FEMS Microbiology Ecology, vol.81, issue.3, pp.507-519, 2012. ,
Genetic structure and isolation by distance in a landrace of thai rice, Proceedings of the National Academy of Sciences, vol.106, issue.33, pp.13880-13885, 2009. ,
Signal transduction in the sexual life of Chlamydomonas, Plant Molecular Biology, vol.26, issue.5, pp.1271-1287, 1994. ,
Metatranscriptomics of the marine sponge Geodia barretti: Tackling phylogeny and function of its microbial community, Environmental Microbiology, vol.14, issue.5, pp.1308-1324, 2012. ,
A review of the biophysical interactions relevant to the promotion of HABs in stratified systems: The case study of Ireland, Deep-Sea Research Part II: Topical Studies in Oceanography, vol.101, pp.21-31, 2014. ,
Community proteomics of a natural microbial biofilm (Supporting Online Material), Science, issue.5730, pp.1915-1920, 2005. ,
, Coupling between taxonomic and functional diversity, 2018.
Pan genome of the phytoplankton Emiliania underpins its global distribution, Nature, issue.7457, pp.209-213, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01074841
Isolation-by-time population structure in potamodromous Dourado Salminus brasiliensis in southern Brazil, Conservation Genetics, vol.18, issue.1, pp.67-76, 2017. ,
Extensive genetic diversity and rapid population differentiation during blooms of alexandrium fundyense (dinophyceae) in an isolated salt pond on cape cod, Ecology and Evolution, vol.2, issue.10, pp.2588-2599, 2012. ,
limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Research, issue.7, p.43, 2015. ,
The Enigma of the Dinoflagellate Chromosome, The Journal of Protozoology, vol.38, issue.3, pp.215-217, 1991. ,
edgeR : differential expression analysis of digital gene expression data, pp.2887-2887, 2011. ,
Differential tolerance among REFERENCES cryptic species: A potential cause of pollutant-related reductions in genetic diversity, Environmental Toxicology and Chemistry, vol.23, issue.9, pp.2132-2137, 2004. ,
Spring arrival along a migratory divide of sympatric blackcaps (Sylvia atricapilla), Oecologia, vol.162, issue.1, pp.175-183, 2010. ,
Large-scale patterns of river inputs in southwestern Europe: Seasonal and interannual variations and potential eutrophication effects at the coastal zone, Biogeochemistry, vol.113, issue.1-3, pp.481-505, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01195671
,
Comparative population genomics in animals uncovers the determinants of genetic diversity, Nature, vol.515, issue.7526, pp.261-263, 2014. ,
Polygenic evolution drives species divergence and climate adaptation in corals, Evolution, vol.72, issue.1, pp.82-94, 2018. ,
,
Fine-scale genetic structure analyses suggest further male than female dispersal in mountain gorillas, BMC Ecology, vol.14, issue.1, pp.70-72, 2014. ,
Revegetation following experimental disturbance in a boreal old-growth Picea abies forest, Journal of Vegetation Science, vol.9, issue.3, pp.763-776, 1998. ,
Spring bloom development, genetic variation, and population succession in the planktonic diatom ditylum brightwellii, Limnology and Oceanography, vol.51, issue.3, pp.1249-1261, 2006. ,
Molecular cloning and immunolocalization of two variants of the major basic nuclear protein (HCc) from the histone-less eukaryote Crypthecodinium cohnii (Pyrrhophyta), Chromosoma, issue.8, pp.510-518, 1991. ,
Inter-and intra-species variation in genome-wide gene expression of Drosophila in response to parasitoid wasp attack, BMC Genomics, vol.18, issue.1, pp.1-14, 2017. ,
Eutrophic waters, algal bloom and fish kill in fish farming areas in, Marine Pollution Bulletin, vol.57, issue.6-12, pp.295-301, 2008. ,
Fossil and living dinoflagellates, 1974. ,
Phenotypic evolution: a reaction norm perspective, 1998. ,
,
When rare species become endangered: Cryptic speciation in myrmecolphilous hoverflies, Journal of the Linnean Society, vol.75, pp.291-300, 2002. ,
Comptes rendus hebdomadaires des séances de l ' Académie des sciences . Série B. Comptes rendus hebdomadaires des séances de l ' Académie des sciences, Série B, vol.275, pp.319-321, 1972. ,
Priority effects in a planktonic bloom-forming marine diatom, Biology letters, vol.11, issue.5, 2015. ,
Local and global factors affecting RNA sequencing analysis, Analytical Biochemistry, vol.419, issue.2, pp.317-322, 2011. ,
Mg2+-independent hairpin ribozyme catalysis in hydrated RNA films, Rna, vol.6, issue.2, pp.189-198, 2000. ,
Seasonal Polyphenism, Evolutionary biology, pp.259-333, 1976. ,
,
Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade, Environmental Microbiology, vol.16, issue.9, pp.2815-2830, 2014. ,
Metatranscriptome sequencing and analysis of agriculture soil provided significant insights about the microbial community structure and function, Ecological Genetics and Genomics, issue.6, pp.9-15, 2017. ,
Capping of eucaryotic mRNAs, Cell, vol.9, issue.4 PART 2, pp.645-653, 1976. ,
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean, 2011. ,
, Isme Journal, vol.5, issue.6, p.000295688200006
The Dinoflagellate Chromosome, Advances in Botanical Research, vol.12, pp.205-264, 1986. ,
Genetic diversity affects ecological performance and stress response of marine diatom populations, The ISME Journal, vol.10, issue.11, pp.2755-2766, 2016. ,
In situ gene expression by Vibrio vulnificus, Applied and Environmental Microbiology, vol.72, issue.3, pp.2244-2246, 2006. ,
On an extremely dense bloom of the dinoflagellate Alexandrium tamarense in lagoons of the po river delta: Impact on the environment, Journal of Sea Research, vol.35, issue.4, pp.90752-90754, 1996. ,
Resource Competition Affects Plankton Community Structure; Evidence from Trait-Based Modeling, Frontiers in Marine Science, vol.4, pp.1-14, 2017. ,
, Dinoflagellate Nuclei, 1984.
Environmental barcoding reveals massive dinoflagellate diversity in marine environments, PLoS ONE, issue.11, p.5, 2010. ,
Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities, 2011. ,
, Genome Biology, vol.12, issue.3
Roles of ion transport in control of cell motility, Comprehensive Physiology, vol.3, issue.1, pp.59-119, 2013. ,
Plants with longer-lived seeds have lower local extinction rates in grassland remnants 1950-1985, Oecologia, vol.120, issue.4, pp.539-543, 1999. ,
Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water, Molecular Ecology, vol.19, issue.1, pp.21-31, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00497208
Dinoflagellates collected from aquaculture ponds in southern Taiwan, Jpn. J. Phycol, vol.39, pp.227-238, 1991. ,
Evidence for Trans splicing in trypanosomes, Cell, vol.47, issue.4, pp.90617-90620, 1986. ,
Evolution of a Polyphenism by Genetic Accommodation, Science, issue.5761, pp.650-652, 2006. ,
A role for phenotypic plasticity in the evolution of aposematism, Proceedings of the Royal Society B: Biological Sciences, vol.269, pp.1639-1644, 1501. ,
Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley, Scientific Reports, issue.6, pp.1-7, 2015. ,
Differential expression in rna-seq: a matter of depth, Genome research, p.124321, 2011. ,
The evolution of novel fungal genes from nonretroviral RNA viruses, BMC Biology, vol.7, issue.1, pp.1-11, 2009. ,
Dispersal, philopatry and intergroup relatedness: Fine-scale genetic structure in the white-breasted thrasher, Ramphocinclus brachyurus, Molecular Ecology, vol.15, issue.11, pp.3449-3458, 2006. ,
Motility and orientation of a dinoflagellate, Gymnodium, impaired by solar and ultraviolet radiation, FEMS Microbiol Ecol, vol.102, issue.3/4, pp.167-174, 1993. ,
,
Gene expression in proliferating cells of the dinoflagellate alexandrium catenella (Dinophyceae), Applied and Environmental Microbiology, vol.76, issue.13, pp.4521-4529, 2010. ,
Pseudo-nitzschia physiological ecology, phylogeny, toxicity, monitoring and impacts on ecosystem health, Harmful Algae, vol.14, pp.271-300, 2012. ,
Differential analysis of gene regulation at transcript resolution with RNA-seq, Nature Biotechnology, vol.31, issue.1, pp.46-53, 2013. ,
Marine population connectivity identifies ecological neighbors for conservation planning in the Coral Triangle, Conservation Letters, vol.5, issue.6, pp.441-449, 2012. ,
Epigenetic inheritance and the missing heritability, Human genomics, vol.9, 2015. ,
Gene expression variation between mouse inbred strains, BMC Genomics, vol.5, pp.1-8, 2004. ,
Community structure and metabolism through reconstruction of microbial genomes from the environment, Nature, vol.428, issue.6978, pp.37-43, 2004. ,
Temporal order of RNA-processing reactions in trypanosomes: rapid trans splicing precedes polyadenylation of newly synthesized tubulin transcripts, Molecular and Cellular Biology, vol.13, issue.1, pp.720-725, 1993. ,
The selection of microbial communities by constant or fluctuating temperatures, FEMS Microbiology Letters, vol.74, issue.4, pp.243-252, 1990. ,
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome, PLoS ONE, issue.6, p.3, 2008. ,
Morphological variation in Plantago lanceolata : limits of plasticity, Evol. Trends Plants, vol.4, pp.35-43, 1990. ,
De novo transcriptome assembly and SNP discovery in the wing polymorphic Salt Marsh beetle pogonus chalceus (Coleoptera, Carabidae), PLoS ONE, issue.8, p.7, 2012. ,
Diversity of marine and freshwater algal toxins, Seafood and freshwater toxins, pp.43-71, 2000. ,
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing, Molecular Ecology, vol.17, issue.7, pp.1636-1647, 2008. ,
Phylogenetic analysis of pseudochlorodesmis strains reveals cryptic diversity above the family level in the siphonous green algae (bryopsidales, chlorophyta), Journal of Phycology, vol.45, issue.3, pp.726-731, 2009. ,
A comparative study on recurrent blooms of Alexandrium REFERENCES minutum in two Mediterranean coastal areas, Harmful Algae, vol.4, issue.4, pp.673-695, 2005. ,
Genetic assimilation of an acquired character, Evolution, vol.7, issue.2, pp.118-126, 1953. ,
Genetic assimilation, Advances in genetics, vol.10, pp.257-93, 1961. ,
Dinoflagellate mitochondrial genomes: Stretching the rules of molecular biology, BioEssays, vol.31, issue.2, pp.237-245, 2009. ,
Neurotoxins from marine dinoflagellates: A brief review, Marine Drugs, vol.6, issue.2, pp.349-371, 2008. ,
Rna-seq: a revolutionary tool for transcriptomics, Nature reviews genetics, vol.10, issue.1, p.57, 2009. ,
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite, Nature, vol.450, issue.7169, pp.560-565, 2007. ,
Species concepts and phylogenetic theory: a debate, 2000. ,
Prokaryotes: The unseen majority, Proceedings of the National Academy of Sciences, vol.95, issue.12, pp.6578-6583, 1998. ,
Conservation biogeography: Assessment and prospect, Diversity and Distributions, vol.11, issue.1, pp.3-23, 2005. ,
Genetic evidence against panmixia in the European eel, Nature, vol.409, issue.6823, pp.1037-1040, 1966. ,
Dinoflagellate Genome Evolution, Annual Review of Microbiology, vol.65, issue.1, pp.369-387, 2011. ,
Phylogenetic structure of the prokaryotic domain: The primary kingdoms, Proceedings of the National Academy of Sciences, vol.74, issue.11, pp.5088-5090, 1977. ,
Trait changes induced by species interactions in two phenotypically distinct strains of a marine dinoflagellate, ISME Journal, vol.10, issue.11, pp.2658-2668, 2016. ,
Population connectivity: dam migration mitigations and contemporary site fidelity in arctic char, BMC Evolutionary Biology, vol.11, issue.1, p.207, 2011. ,
Histone-Like Proteins of the Dino agellate, Society, vol.2, issue.3, pp.646-650, 2003. ,
The evolution of transcriptional regulation in eukaryotes, Molecular Biology and Evolution, vol.20, issue.9, pp.1377-1419, 2003. ,
Notes on Alexandrium population dynamics, doi: Article Wyatt, vol.28, pp.551-575, 1943. ,
,
Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries, ISME Journal, vol.5, issue.3, pp.414-426, 2011. ,
Transcriptional responses of invasive and indigenous whiteflies to different host plants reveal their disparate capacity of adaptation, Scientific Reports, issue.5, pp.1-14, 2014. ,
Role of wind in regulating phytoplankton blooms on the Mid-Atlantic Bight. (Mld), 2012. ,
Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum, BMC Genomics, issue.1, p.11, 2010. ,
Molecular phylogenetics: Principles and practice, Nature Reviews Genetics, vol.13, issue.5, pp.303-314, 2012. ,
Involvement of calcium mobilization from caffeine-sensitive stores in mechanically induced cell cycle arrest in the dinoflagellate Crypthecodinium cohnii, Cell Calcium, vol.39, issue.3, pp.259-274, 2006. ,
The first finding of toxic dinoflagellate Alexandrium minutum in Vietnam, Fisheries Science, vol.66, issue.1, pp.177-179, 2000. ,
In vitro culture significantly alters gene expression profiles and reduces differences between myometrial and fibroid smooth muscle cells, Molecular Human Reproduction, vol.12, issue.3, pp.187-207, 2006. ,
Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles, Scientific Reports, vol.6, pp.1-11, 2016. ,
Spliced leader RNA trans-splicing in dinoflagellates, Proceedings of the National Academy of Sciences, vol.104, pp.4618-4623, 2007. ,
Single gene circles in dinoflagellate chloroplast genomes, Nature, vol.400, issue.6740, pp.155-159, 1999. ,
Responses of a coastal phytoplankton community to increased nutrient input from the Changjiang, vol.28, pp.1483-1489, 2008. ,
Atlas of modern dinoflagellate cyst distribution based on 2405 data points, Review of Palaeobotany and Palynology, vol.191, pp.1-197, 2013. ,