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51. In search of new tractable diatoms for experimental biology

Author

Pieter Vanormelingen, Koen Sabbe, Wim Vyverman, Peter von Dassow, Victor A. Chepurnov, Dirk Inzé, Jeroen Gillard, and David G. Mann

Subjects
Diatoms, Experimental control, biology, Ecology, Reproduction, Context (language use), Biological evolution, Mating system, biology.organism_classification, Biological Evolution, General Biochemistry, Genetics and Molecular Biology, Pedigree, Cell size, Diatom, Models, Animal, Ecological significance, Animals, Experimental biology, Ecosystem, Phylogeny
Abstract

Diatoms are a species-rich group of photosynthetic eukaryotes, with enormous ecological significance and great potential for biotechnology. During the last decade, diatoms have begun to be studied intensively using modern molecular techniques and the genomes of four diatoms have been wholly or partially sequenced. Although new insights into the biology and evolution of diatoms are accumulating rapidly due to the availability of reverse genetic tools, the full potential of these molecular biological approaches can only be fully realized if experimental control of sexual crosses becomes firmly established and widely accessible to experimental biologists. Here we discuss the issue of choosing new models for diatom research, by taking into account the broader context of diatom mating systems and the place of sex in relation to the intricate cycle of cell size reduction and restitution that is characteristic of most diatoms. We illustrate the results of our efforts to select and develop experimental systems in diatoms, using species with typical life cycle attributes, which could be used as future model organisms to complement existing ones.

Published
2008
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53. Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

Author

Sara Moeys, Remo Sanges, Daniel Mapleson, Marina Montresor, Maria Immacolata Ferrante, Peter von Dassow, Marie J. J. Huysman, Wim Vyverman, Shrikant Patil, Lieven De Veylder, Stazione Zoologica Anton Dohrn (SZN), Universiteit Gent = Ghent University (UGENT), Flanders Institute for Biotechnology, Universiteit Gent = Ghent University (UGENT)-Department of Plant Systems Biology, Evolutionary Biology and Ecology of Algae (EBEA), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS), Instituto Milenio de Oceanografia (IMO), Pontificia Universidad Católica de Chile (UC), Departamento de Ecologia, The Genome Analysis Centre (TGAC), Department of Plant Systems Biology, Department of Plant Biotechnology and Bioinformatics, Department of Biology (Terrestrial Ecology Unit) (Ghent University), Universiteit Gent = Ghent University [Belgium] (UGENT), Universiteit Gent = Ghent University [Belgium] (UGENT)-Department of Plant Systems Biology, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC), Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile, and Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile-Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile

Subjects
BUDDING YEAST, Thalassiosira pseudonana, Gene Expression, Cell Cycle Proteins, DOUBLE-STRAND BREAKS, Chromosomal crossover, THALASSIOSIRA-PSEUDONANA, GENE DUPLICATION, SACCHAROMYCES-CEREVISIAE, CROSSING-OVER, 03 medical and health sciences, 0302 clinical medicine, Meiosis, EVOLUTIONARY HISTORY, Phylogenetics, Settore BIO/13 - Biologia Applicata, Genetics, Sexual reproduction, SYNAPTONEMAL COMPLEX, Phaeodactylum tricornutum, Phylogeny, 030304 developmental biology, Diatoms, 0303 health sciences, biology, Synaptonemal Complex, Reproduction, fungi, Biology and Life Sciences, Proteins, Correction, DNA MISMATCH REPAIR, biology.organism_classification, SPO11, CHROMOSOME SYNAPSIS, Diatom, RAD51, DMC1, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery, Biotechnology
Abstract

Background Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. Results The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestral loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. Conclusions Our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.

Published
2015
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54. RELATIONSHIPS BETWEEN GROWTH RATE, CELL SIZE, AND INDUCTION OF SPERMATOGENESIS IN THE CENTRIC DIATOMTHALASSIOSIRA WEISSFLOGII(BACILLARIOPHYTA)

Author

Victor A. Chepurnov, Peter von Dassow, and E. Virginia Armbrust

Subjects
Cell Enlargement, Plant Science, Aquatic Science, Biology, biology.organism_classification, Sperm, Andrology, Human fertilization, Multinucleate, Thalassiosira weissflogii, Botany, Growth rate, Spermatogenesis, Cytokinesis
Abstract

Patterns of changes in cell size, growth rate, and the inducibility of spermatogenesis were followed in eight sub-clones of two isolates of the centric diatom Thalassiosira weissflogii (Grunow) Fryxell & Hasle grown at saturating light. One isolate originated from Long Island Sound, New York, USA and the other originated from Jakarta Harbor, Indonesia. As expected from previous studies, oscillations between intervals of cell size reduction and cell size enlargement were observed for each sub-clone. For both isolates, sperm were easily detected, but cells resembling eggs and auxospores were rarely observed and fertilization was not confirmed, suggesting that the observed cell size increases may have resulted from a combination of asexual cell enlargement and rare auxosporulation. The two isolates differed in their minimum and maximum sizes, and the threshold size for the induction of sperm formation. However, the two sets of isolated sub-clones displayed comparable relationships between growth rate, sperm inducibility, and cell size relative to the minimum, maximum, and threshold sizes. Growth rate increased as cell size decreased during vegetative divisions until the threshold for sperm inducibility was crossed. Below the size threshold for sperm inducibility, growth rate declined as cell size continued to decrease. Smaller cells were susceptible to failure of normal cytokinesis and valve deposition, resulting in the formation of abnormally long and often multinucleate cells. Culture conditions may select against restoration of cell size via auxosporulation due to the relationship between growth rate and cell size.

Published
2006
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55. Bioluminescent response of the dinoflagellate Lingulodinium polyedrum to developing flow: Tuning of sensitivity and the role of desensitization in controlling a defensive behavior of a planktonic cell

Author

R. N. Bearon, Michael I. Latz, and Peter von Dassow

Subjects
medicine.medical_treatment, Dinoflagellate, Laminar flow, Aquatic Science, Biology, Oceanography, biology.organism_classification, Shear (sheet metal), Botany, Biophysics, medicine, Bioluminescence, Bloom, Lingulodinium polyedrum, Couette flow, Desensitization (medicine)
Abstract

Dinoflagellate bioluminescence is believed to serve a defensive function, decreasing grazing at night. Previous characterization of bioluminescence stimulated by fully developed flows might have underestimated the true sensitivity of bioluminescence by not observing the initial response. Also, it has been suggested that bioluminescence may be more sensitive to time-varying flow than to constant flow conditions. We used developing laminar Couette flow to characterize the sensitivity of the initial bioluminescent response of the dinoflagellate Lingulodinium polyedrum in time-varying flow. Both the absolute sensitivity (threshold) and dynamic sensitivity were consistent with that determined previously in fully developed flows, although there were differences between different cultured isolates of the same species and between those isolates and cells harvested from a unialgal bloom of the same species. When the rate of increase of shear was varied while keeping the maximum shear level similar, the threshold was independent of the rate of increase of shear. Surprisingly, the integrated bioluminescence was strongly dependent on the rate of increase of shear. The mechanism behind the preferential response to rapidly increasing shear was determined to be desensitization. Desensitization may influence which naturally occurring flows strongly stimulate bioluminescence either by allowing cells to avoid producing a primary response in certain slowly changing flows or, more generally, to avoid the cost of repeated stimulation when entrained in environmental flows containing above-threshold shears.

Published
2005
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56. The role of Ca2+ in stimulated bioluminescence of the dinoflagellateLingulodinium polyedrum

Author

Michael I. Latz and Peter von Dassow

Subjects
Ruthenium red, Physiology, Stimulation, Aquatic Science, Biology, chemistry.chemical_compound, Extracellular, Animals, Seawater, Luciferase, Mechanotransduction, Egtazic Acid, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Chelating Agents, Analysis of Variance, Ionomycin, biology.organism_classification, Calcium Ionophores, Ruthenium Red, Kinetics, Digitonin, chemistry, Biochemistry, Insect Science, Luminescent Measurements, Dinoflagellida, Potassium, Biophysics, Calcium, Animal Science and Zoology, Lingulodinium polyedrum
Abstract

SUMMARYMany marine dinoflagellates emit bright discrete flashes of light nearly instantaneously in response to either laminar or turbulent flows as well as to direct mechanical stimulation. The flash involves a unique pH-dependent luciferase and a proton-mediated action potential across the vacuole membrane. The mechanotransduction process initiating this action potential is unknown. The present study investigated the role of Ca2+ in the mechanotransduction process regulating bioluminescence in the dinoflagellate Lingulodinium polyedrum. Calcium ionophores and digitonin stimulated luminescence in a Ca2+-dependent manner in the absence of mechanical stimulation. Mechanically sensitive luminescence was strongly inhibited by the intracellular Ca2+ chelator BAPTA-AM[1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid acetoxymethyl ester]; there was only a partial and irreversible dependence on extracellular Ca2+. Ruthenium Red, a blocker of intracellular Ca2+ release channels, inhibited mechanically sensitive luminescence. Luminescence was also stimulated by increasing K+, even in the absence of extracellular Ca2+; K+ stimulation was inhibited both by BAPTA-AM and Ruthenium Red. These results support the hypothesis that Ca2+mediates stimulated bioluminescence and also indicate the involvement of intracellular Ca2+ stores. Rapid coupling between mechanical stimulation and mobilization of intracellular Ca2+ stores might occur through a mechanism similar to excitation-contraction coupling in skeletal muscle.

Published
2002
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57. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

Author

Peter, von Dassow, Uwe, John, Hiroyuki, Ogata, Ian, Probert, El Mahdi, Bendif, Jessica U, Kegel, Stéphane, Audic, Patrick, Wincker, Corinne, Da Silva, Jean-Michel, Claverie, Scott, Doney, David M, Glover, Daniella Mella, Flores, Yeritza, Herrera, Magali, Lescot, Marie-José, Garet-Delmas, and Colomban, de Vargas

Subjects
Chlorophyll, Genetic Markers, Life Cycle Stages, Genome, Ecology, Genotype, Gene Expression Profiling, Oceans and Seas, fungi, Computational Biology, Haptophyta, Genomics, Diploidy, Flagella, Phytoplankton, Animals, Original Article, Biomass
Abstract

Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.

Published
2014

58. Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis

Author

Peter von Dassow, Björn Rost, Sebastian D. Rokitta, Uwe John, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Pontificia Universidad Católica de Chile (UC), Evolutionary Biology and Ecology of Algae (EBEA), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Nitrogen, Respiratory chain, Haploidy, Emiliania huxleyi, Microarray, Photosynthesis, 01 natural sciences, Electron Transport, Transcriptome, 03 medical and health sciences, Adenosine Triphosphate, Nutrient, Lipid oxidation, Genetics, Polyamines, Transcriptomics, 030304 developmental biology, 0303 health sciences, Malate:quinone-oxidoreductase, biology, Phototroph, Gene Expression Profiling, 010604 marine biology & hydrobiology, fungi, Haptophyta, Proline oxidation, Limitation, biology.organism_classification, Diploidy, Carbon, Diatom, Metabolism, Biochemistry, Protein Biosynthesis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Energy Metabolism, Metabolic Networks and Pathways, Ornithine-urea-cycle, Research Article, Biotechnology
Abstract

Background Global change will affect patterns of nutrient upwelling in marine environments, potentially becoming even stricter regulators of phytoplankton primary productivity. To better understand phytoplankton nutrient utilization on the subcellular basis, we assessed the transcriptomic responses of the life-cycle stages of the biogeochemically important microalgae Emiliania huxleyi to nitrogen-limitation. Cells grown in batch cultures were harvested at ‘early’ and ‘full’ nitrogen-limitation and were compared with non-limited cells. We applied microarray-based transcriptome profilings, covering ~10.000 known E. huxleyi gene models, and screened for expression patterns that indicate the subcellular responses. Results The diploid life-cycle stage scavenges nitrogen from external organic sources and -like diatoms- uses the ornithine-urea cycle to rapidly turn over cellular nitrogen. The haploid stage reacts similarly, although nitrogen scavenging is less pronounced and lipid oxidation is more prominent. Generally, polyamines and proline appear to constitute major organic pools that back up cellular nitrogen. Both stages induce a malate:quinone-oxidoreductase that efficiently feeds electrons into the respiratory chain and drives ATP generation with reduced respiratory carbon throughput. Conclusions The use of the ornithine-urea cycle to budget the cellular nitrogen in situations of limitation resembles the responses observed earlier in diatoms. This suggests that underlying biochemical mechanisms are conserved among distant clades of marine phototrophic protists. The ornithine-urea cycle and proline oxidation appear to constitute a sensory-regulatory system that monitors and controls cellular nitrogen budgets under limitation. The similarity between the responses of the life-cycle stages, despite the usage of different genes, also indicates a strong functional consistency in the responses to nitrogen-limitation that appears to be owed to biochemical requirements. The malate:quinone-oxidoreductase is a genomic feature that appears to be absent from diatom genomes, and it is likely to strongly contribute to the uniquely high endurance of E. huxleyi under nutrient limitation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1051) contains supplementary material, which is available to authorized users.

Published
2014
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59. Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond at Cahuil Lagoon, Chile

Author

Daniel Vaulot, Marine Blanchet, Marcia Astorga, Carlos Henríquez-Castillo, Gerrit van den Engh, María Lorena González, Priscila Ikeda, Claudia Elizondo-Patrone, Florencia Bertoglio, Felipe Docmac, Nicole Trefault, María Jesús Gálvez, Fernando Guido Sorroche, Silvia Narváez, Yolaine Delgado, Rodrigo De la Iglesia, Francisco Santibañez, Kurt Hanselmann, Eric E. Allen, Osvaldo Ulloa, Nathalie Delherbe, Marcelo Rojas-Herrera, Alvaro M. Plominsky, Peter von Dassow, Juan A. Ugalde, Adriana Lopes do Santos, Carla Gimpel, Pontificia Universidad Católica de Chile (UC), Facultad de Ciencias, Marine Biology Research Division, University of California [San Diego] (UC San Diego), University of California-University of California-Scripps Institution of Oceanography, Division of Biological Sciences [San Diego], University of California-University of California, Biogeochemistry and Microbiology, Polytechnic School of the University of São Paulo (Brazil), Universidade de São Paulo (USP), Universidad de Concepción [Chile], Geological Institute [ETH Zürich], Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Departmento de Oceanografía & Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biomedical Research Center in Bioengineering, Biomaterials, and Nanomedicine ( (CIBER-BBN), Biomedical Research Center, Biomedical Image Technologies Lab, ETSI Telecomunicación, Universidad Politécnica de Madrid (UPM), BD Advanced Cytometry Group, Instituto Antartico Chileno, Centro Universitario Regional Este, Universidad de La Habana [Cuba], Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Ecologıa y Recursos Naturales, Instituto de Investigaciones Marinas y Costeras 'José Benito Vives de Andréis' (INVEMAR), Ministerio del Medio Ambiente, Colombie, Facultad de Ciencias Exactas y Naturales [Mar del Plata], Universidad Nacional de Mar del Plata [Mar del Plata] (UNMdP), Scripps Institution of Oceanography (SIO - UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), School of Biological Sciences [Univ California San Diego] (UC San Diego), Universidade de São Paulo = University of São Paulo (USP), and Universidad de Concepción - University of Concepcion [Chile]

Subjects
0303 health sciences, 030306 microbiology, Ecology, [SDV]Life Sciences [q-bio], education, fungi, Biology, Microbiology, Salinity, 03 medical and health sciences, Microbial population biology, Metagenomics, parasitic diseases, [SDE]Environmental Sciences, Genetics, Prokaryotes, Biochemistry and Cell Biology, Molecular Biology, 030304 developmental biology
Abstract

Cáhuil Lagoon in central Chile harbors distinct microbial communities in various solar salterns that are arranged as interconnected ponds with increasing salt concentrations. Here, we report the metagenome of the 3.0- to 0.2-µm fraction of the microbial community present in a crystallizer pond with 34% salinity.

Published
2014
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60. In Situ Tolerance within the Central Nervous System as a Mechanism for Preventing Autoimmunity

Author

Peter von Dassow, Nadia Ordonez, Thea Brabb, Bryan Schnabel, Blythe Duke, and Joan Goverman

Subjects
Central Nervous System, Multiple Sclerosis, T cell, Genes, RAG-1, T-Lymphocytes, Immunology, Receptors, Antigen, T-Cell, Mice, Transgenic, Biology, Immune tolerance, Interleukin 21, Mice, Antigen, trafficking, medicine, Immune Tolerance, Immunology and Allergy, Cytotoxic T cell, Animals, Crosses, Genetic, transgenic, Homeodomain Proteins, Mice, Knockout, T-cell receptor, experimental allergic encephalomyelitis, CD28, Myelin Basic Protein, Myelin basic protein, Mice, Inbred C57BL, medicine.anatomical_structure, biology.protein, Original Article
Abstract

Multiple sclerosis (MS) is believed to be an autoimmune disease in which autoreactive T cells infiltrate the central nervous system (CNS). Animal models of MS have shown that CNS-specific T cells are present in the peripheral T cell repertoire of healthy mice and cause autoimmune disease only when they are activated by immunization. T cell entry into the CNS is thought to require some form of peripheral activation because the blood–brain barrier prohibits trafficking of this tissue by naive cells. We report here that naive T cells can traffic to the CNS without prior activation. Comparable numbers of T cells are found in the CNS of both healthy recombinase activating gene (Rag)−/− T cell receptor (TCR) transgenic mice and nontransgenic mice even when the transgenic TCR is specific for a CNS antigen. Transgenic T cells isolated from the CNS that are specific for non-CNS antigens are phenotypically naive and proliferate robustly to antigenic stimulation in vitro. Strikingly, transgenic T cells isolated from the CNS that are specific for myelin basic protein (MBP) are also primarily phenotypically naive but are unresponsive to antigenic stimulation in vitro. Mononuclear cells from the CNS of MBP TCR transgenic but not nontransgenic mice can suppress the response of peripheral MBP-specific T cells in vitro. These results indicate that naive MBP-specific T cells can traffic to the CNS but do not trigger autoimmunity because they undergo tolerance induction in situ.

Published
2000

61. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author

Jean-Marc Aury, Frithjof C. Küpper, Diego Miranda-Saavedra, John H. F. Bothwell, Claire Jubin, Chris Bowler, Bernhard Gschloessl, James W. Tregear, Andrés Ritter, Andrew E. Allen, Carolyn A. Napoli, Ludovic Delage, Bernard Kloareg, Takahiro Yamagishi, Pi Nyvall-Collén, Svenja Heesch, Julia Morales, Gaelle Samson, Kei Kimura, Ga Youn Cho, Grigoris D. Amoutzias, Yves Van de Peer, Simon M. Dittami, Kenny Billiau, Julie Poulain, François Artiguenave, Sylvie Doulbeau, Marek Eliáš, Bank Beszteri, Carl J. Carrano, Daniel Lang, Florian Maumus, Stefan A. Rensing, Jonathan H. Badger, Béatrice Segurens, Martina Strittmatter, Sylvie Rousvoal, Hervé Moreau, Patrice Lerouge, Colin Brownlee, Betsy Read, Akira F. Peters, J. Mark Cock, Corinne Da Silva, Declan C. Schroeder, Catherine Boyen, Pierre Rouzé, Eric Bonnet, Jonas Collén, Susana M. Coelho, Aude Le Bail, Kamel Jabbari, David R. Nelson, Thierry Tonon, Pascal J. Lopez, Véronique Anthouard, Hadi Quesneville, Manoj P. Samanta, Delphine Scornet, Klaus Valentin, Nicolas Delaroque, Bénédicte Charrier, Cindy Martens, Peter von Dassow, Martin Lohr, Garry Farnham, Chikako Nagasato, Claire M. M. Gachon, Gurvan Michel, Lieven Sterck, Philippe Potin, Erwan Corre, Catherine Leblanc, Taizo Motomura, Cyril Pommier, Patrick Wincker, Hiroshi Kawai, Publica, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, J Craig Venter Institute, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Marine Biological Association, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), San Diego State University (SDSU), Phophorylation de protéines et Pathologies Humaines (P3H), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Charles University [Prague], Scottish Association for Marine Science (SAMS), Kobe University, Institute of Algological Research [Muroran], Hokkaido University, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Johannes Gutenberg - Universität Mainz (JGU), École normale supérieure - Paris (ENS Paris), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Haematology, University of Cambridge [UK] (CAM), Mer et santé (MS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Arizona, The University of Tennessee Health Science Center [Memphis] (UTHSC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), California State University [Los Angeles] (CAL STATE LA), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Systemix Institute, Savelli, Bruno, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), J. Craig Venter Institute, Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Charles University [Prague] (CU), Hokkaido University [Sapporo, Japan], Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris

Subjects
0106 biological sciences, Lineage (evolution), Molecular Sequence Data, Phaeophyta, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Algae, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Botany, BIOLOGIE CELLULAIRE, Animals, 14. Life underwater, [SDV.BDD]Life Sciences [q-bio]/Development Biology, flore marine, Phylogeny, Organism, ComputingMilieux_MISCELLANEOUS, phéophycées, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Ectocarpus siliculosus, Algal Proteins, Eukaryota, Pigments, Biological, Ectocarpus, 15. Life on land, biology.organism_classification, Biological Evolution, Brown algae, Multicellular organism, Evolutionary biology, algues brunes, Biologie, Signal Transduction, 010606 plant biology & botany
Abstract

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. © 2010 Macmillan Publishers Limited. All rights reserved.

Published
2010
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62. Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

Author

Peter von Dassow, Ian Probert, Stéphane Audic, Patrick Wincker, Hiroyuki Ogata, Jean-Michel Claverie, Colomban de Vargas, Corinne Da Silva, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme [PIIF-GA-2008221812], Actions Thematique et Incitatives sur Programme (ATIP), Centre National de la Recherche Scientifique, France, French Agence Nationale de la Recherche [ANR-05-BIODIV-004], PACA-BioInfo Platform, and Marseille-Nice Genopole

Subjects
0106 biological sciences, Time Factors, [SDV]Life Sciences [q-bio], Haploidy, 01 natural sciences, Histones, Transcriptome, Histone H4, 03 medical and health sciences, Sequence Homology, Nucleic Acid, Cluster Analysis, 14. Life underwater, Photosynthesis, Gene, Gene Library, 030304 developmental biology, Emiliania huxleyi, Expressed Sequence Tags, Genetics, 0303 health sciences, Expressed sequence tag, biology, Reverse Transcriptase Polymerase Chain Reaction, cDNA library, Gene Expression Profiling, Research, 010604 marine biology & hydrobiology, Cell Cycle, fungi, Membrane Transport Proteins, Reproducibility of Results, Flow Cytometry, biology.organism_classification, Diploidy, Gene Expression Regulation, Mating of yeast, Flagella, Phytoplankton, [SDE]Environmental Sciences, Ploidy
Abstract

An EST analysis of the phytoplankton Emiliania huxleyi reveals genes involved in haploid- and diploid-specific processes and provides insights into environmental adaptation., Background Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38,000 expressed sequence tags from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism. Results The haploid and diploid transcriptomes showed a dramatic differentiation, with approximately 20% greater transcriptome richness in diploid cells than in haploid cells and only ≤ 50% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog. Conclusions This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined.

Published
2009
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63. Phytoplankton calcification in a high-CO2 world

Author

Samantha J. Gibbs, Elena Colmenero-Hidalgo, Rosalind E. M. Rickaby, Peter von Dassow, Ian Hall, Darryl R H Green, Paul R. Halloran, Eric Rehm, Karin P. Boessenkool, E. Virginia Armbrust, John R. Gittins, Toby Tyrrell, and M. Debora Iglesias-Rodriguez

Subjects
0106 biological sciences, Geologic Sediments, 010504 meteorology & atmospheric sciences, Coccolithophore, Oceans and Seas, 01 natural sciences, Deep sea, Calcium Carbonate, Coccolith, Calcification, Physiologic, Phytoplankton, 14. Life underwater, Photosynthesis, 0105 earth and related environmental sciences, Emiliania huxleyi, Multidisciplinary, biology, Atmosphere, Ecology, 010604 marine biology & hydrobiology, fungi, Eukaryota, Global change, Ocean acidification, Carbon Dioxide, Hydrogen-Ion Concentration, Plankton, biology.organism_classification, Oceanography, 13. Climate action
Abstract

Ocean acidification in response to rising atmospheric CO 2 partial pressures is widely expected to reduce calcification by marine organisms. From the mid-Mesozoic, coccolithophores have been major calcium carbonate producers in the world's oceans, today accounting for about a third of the total marine CaCO 3 production. Here, we present laboratory evidence that calcification and net primary production in the coccolithophore species Emiliania huxleyi are significantly increased by high CO 2 partial pressures. Field evidence from the deep ocean is consistent with these laboratory conclusions, indicating that over the past 220 years there has been a 40% increase in average coccolith mass. Our findings show that coccolithophores are already responding and will probably continue to respond to rising atmospheric CO 2 partial pressures, which has important implications for biogeochemical modeling of future oceans and climate.

Published
2008

64. The $Phaeodactylum$ genome reveals the evolutionary history of diatom genomes

Author

Yves Van de Peer, Michael R. Sussman, Frédéric Verret, Miyoshi Haruta, Angela Falciatore, John A. Berges, Leszek Rychlewski, Anusuya Willis, Richard E. Jorgensen, Michael Katinka, Jane Grimwood, Betina M. Porcel, Magali Siaut, Klaus Valentin, Pascal J. Lopez, Marc Heijde, Véronique Martin-Jézéquel, Jean-Louis Petit, Wim Vyverman, Edda Rayko, Klaas Vandepoele, Miroslav Oborník, Anthony Chiovitti, Alan Kuo, E. Virginia Armbrust, Matthew Robison, Alessandra De Martino, Nils Kröger, Susan Lucas, Colin Brownlee, Alison Taylor, Igor V. Grigoriev, Jonathan H. Badger, Kamel Jabbari, Jérome Fournet, Jeremy Schmutz, Uma Maheswari, Sacha Coesel, Michele S. Stanley, J. Chris Detter, Chang Jae Choi, Thomas Mock, Assaf Vardi, Markus Lommer, Aaron Kaplan, Yolaine Joubert, Florian Maumus, Katerina Jiroutova, Anton Montsant, Colleen A. Durkin, Cindy Martens, Bank Beszteri, Micaela S. Parker, Asaf Salamov, Linda K. Medlin, Karen M. McGinnis, Ansgar Gruber, Marie J. J. Huysman, Manuela Mangogna, Lucyan S. Wyrwicz, Jean-Paul Cadoret, Peter von Dassow, Daniel S. Rokhsar, Marie-Pierre Oudot-Le Secq, Carolyn A. Napoli, Beverley R. Green, Erica Lindquist, Peter G. Kroth, Chris Bowler, Andrew E. Allen, Tatiana A. Rynearson, Nicole Poulsen, Bethany D. Jenkins, Harris Shapiro, Robert Otillar, Jean Weissenbach, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL), J. Craig Venter Institute, J. Craig Venter Institute [La Jolla, USA] (JCVI), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), DOE Joint Genome Institute [Walnut Creek], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut de biologie de l'Ecole Normale Supérieure (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Biologie moléculaire des organismes photosynthétiques (UMR8186), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Environnement, Bioénergie, Microalgues et Plantes (EBMP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Marine Biological Association, Physiologie et biotechnologie des Algues (PBA), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn (SZN), Génomique des Microorganismes (LGM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Marine Biogeochemistry, Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Biology Institute, University of Arizona, School of Oceanography [Seattle], University of Washington [Seattle], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Station biologique de Roscoff [Roscoff] (SBR), European Project: 29849,DIATOMICS, Savelli, Bruno, Understanding Diatom Biology by Functional Genomics Approaches - DIATOMICS - 29849 - OLD, École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bioénergie et Microalgues (EBM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génomique des microorganismes, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)

Subjects
0106 biological sciences, Thalassiosira pseudonana, Molecular Sequence Data, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, DNA, Algal, Phylogenetics, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, Phaeodactylum tricornutum, Gene, 030304 developmental biology, Genetics, Diatoms, 0303 health sciences, Multidisciplinary, biology, Sequence Homology, Amino Acid, Heterokont, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, biology.organism_classification, Protein Structure, Tertiary, Diatom, Genes, Bacterial, Biologie, 010606 plant biology & botany, Signal Transduction
Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (

Published
2008
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65. Alteration of Sexual Reproduction and Genetic Diversity in the Kelp Species Laminaria digitata at the Southern Limit of Its Range

Author

Peter von Dassow, Marine Robuchon, Stéphane Mauger, Luz Valeria Oppliger, Myriam Valero, Juan A. Correa, Sarah Bouchemousse, Christophe Destombe, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Departamento de Ecologia, Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile, Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile-Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile, Center of applied ecology & sustainability (CAPES), Facultad de ciencias biologicas [Santiago], Pontificia Universidad Católica de Chile (UC)-Pontificia Universidad Católica de Chile (UC), Instituto Milenio de Oceanografia (IMO), Pontificia Universidad Católica de Chile (UC), DIVersité et COnnectivité dans le paysage marin côtier (DIVCO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Reproductive Isolation, Range (biology), Population, Kelp, lcsh:Medicine, Population genetics, Plant Science, 010603 evolutionary biology, 01 natural sciences, Seawater, 14. Life underwater, lcsh:Science, education, Ecosystem, Evolutionary Biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, education.field_of_study, Genetic diversity, Ploidies, Multidisciplinary, Geography, Population Biology, biology, Ecology, Reproduction, 010604 marine biology & hydrobiology, Ecology and Environmental Sciences, lcsh:R, fungi, Temperature, Genetic Variation, Biology and Life Sciences, 15. Life on land, biology.organism_classification, Laminaria digitata, Sexual reproduction, lcsh:Q, Laminaria, Genetic isolate, Microsatellite Repeats, Research Article
Abstract

International audience; Adaptation to marginal habitats at species range-limits has often been associated with parthenogenetic reproduction in terrestrial animals and plants. Laboratory observations have shown that brown algae exhibit a high propensity for parthenogenesis by various mechanisms. The kelp Laminaria digitata is an important component of the ecosystem in Northern European rocky intertidal habitats. We studied four L. digitata populations for the effects of marginality on genetic diversity and sexual reproduction. Two populations were marginal: One (Locquirec, in Northern Brittany) was well within the geographic range, but was genetically isolated from other populations by large stretches of sandy beaches. Another population was at the range limits of the species (Quiberon, in Southern Brittany) and was exposed to much higher seasonal temperature changes. Microsatellite analyses confirmed that these populations showed decreased genetic and allelic diversity, consistent with marginality and genetic isolation. Sporophytes from both marginal populations showed greatly diminished spore-production compared to central populations, but only the southern-limit population (Quiberon) showed a high propensity for producing unreduced (2N) spores. Unreduced 2N spores formed phenotypically normal gametophytes with nuclear area consistent with $2N DNA contents, and microsatellite studies suggested these were produced at least in part by automixis. However, despite this being the dominant path of spore production in Quiberon sporophyte individuals, the genetic evidence indicated the population was maintained mostly by sexual reproduction. Thus, although spore production and development showed the expected tendency of geographical parthenogenesis in marginal populations, this appeared to be a consequence of maladaptation, rather than an adaptation to, life in a marginal habitat.

Published
2014
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66. Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)

Author

Jarred E. Swalwell, Peter von Dassow, Julie A. Koester, E. Virginia Armbrust, School of Oceanography [Seattle], University of Washington [Seattle], Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Species complex, Northwestern United States, Range (biology), Evolution, Genetic Speciation, media_common.quotation_subject, Population, 010603 evolutionary biology, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, DNA, Algal, Gene Duplication, Research article, QH359-425, education, Genome size, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, media_common, Diatoms, 0303 health sciences, education.field_of_study, biology, Sequence Analysis, DNA, biology.organism_classification, Speciation, Ditylum brightwellii, Diatom, Genetics, Population, Evolutionary biology, New Zealand
Abstract

Background Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. Results All isolates from the more regionally-localized population (population 2) possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. Conclusions The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms.

Published
2010
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