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86 results on '"Stéphane Audic"'

1. Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene

Author: Bernard Lasserre, Daniel Grzebyk, Colomban de Vargas, Eric Abadie, Béatrice Bec, Stéphane Audic, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, 0301 basic medicine, alexandrium dinophyceae, Monitoring, Harmful Algal Bloom, [SDE.MCG]Environmental Sciences/Global Changes, Phytoplankton diversity, pseudo-nitzschia bacillariophyceae, Plant Science, Aquatic Science, 01 natural sciences, eastern adriatic sea, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Mediterranean sea, species complex dinophyceae, RNA, Ribosomal, 28S, Phytoplankton, Mediterranean Sea, Akashiwo sanguinea, DNA Barcoding, Taxonomic, Harmful algae, Biomass, 14. Life underwater, phylogenetic-relationships, Ecosystem, Phylogeny, pfiesteria-piscicida dinophyceae, Geography, biology, Ecology, 010604 marine biology & hydrobiology, dinoflagellate stoeckeria-changwonensis, Dinophysis acuminata, Dinoflagellate, High-Throughput Nucleotide Sequencing, Genes, rRNA, biology.organism_classification, 030104 developmental biology, Diatom, domoic acid accumulation, Dinoflagellida, Metabarcoding, Pfiesteria piscicida, Pyrosequencing, partial lsu rdna, toxic dinoflagellate, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; This study investigated the genetic diversity of phytoplankton communities in six shallow lagoons located on the French coast of the northwestern Mediterranean Sea that represented a trophic gradient ranging from oligotrophic to hypereutrophic. The phytoplankton communities were sampled once a month from spring (May) to the beginning of autumn (September/early October) in 2012 and fractionated by size. Metabarcodes were generated from cDNAs by targeting the D1-D2 region of the 28S rRNA gene and pyrosequenced using Roche 454 technology. Examination of the annotated barcodes revealed harmful algal species not previously documented in these lagoons. Three ichthyotoxic species belonging to Pfiesteriaceae were detected: Luciella masanensis was relatively widespread and abundant in many samples, whereas Pfiesteria piscicida and Stoeckeria changwonensis were found as single barcode sequences. Furthermore, a phylogenetic analysis of barcodes annotated as belonging to Pfiesteriaceae suggested the existence of two previously undescribed clades. The other toxic or potentially harmful dinoflagellates detected through rare barcodes were Dinophysis acuminata, Vulcanodinium rugosum, Alexandrium andersonii and A. ostenfeldii. The two most abundant dinoflagellate taxa were Gymnodinium litoralis and Akashiwo sanguinea with respect to sequence numbers. Four diatom species from the genus Pseudo-nitzschia that potentially produce domoic acid were identified (P. galaxiae, P. delicatissima, P. brasiliana and P. calliantha). These observations are discussed in terms of the literature and monitoring records related to the identified taxa in this Mediterranean area.
Published: 2017
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2. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.)

Author: Stéphane Audic, Daniel J. Richter, Colomban de Vargas, Xavier Pochon, Cédric Berney, Johan Decelle, Solenn Mordret, Sébastien Colin, Nicolas Henry, Sarah Romac, Margaux Carmichael, 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Genotype, Oceans and Seas, [SDV]Life Sciences [q-bio], DNA, Ribosomal, Microbiology, 03 medical and health sciences, Symbiodinium, Microbial ecology, Animals, DNA Barcoding, Taxonomic, 14. Life underwater, Ciliophora, Symbiosis, Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, Ecology, Geography, biology, fungi, Dinoflagellate, Marine habitats, Pelagic zone, Biodiversity, Plankton, biology.organism_classification, Biological Evolution, 030104 developmental biology, Haplotypes, Benthic zone, [SDE]Environmental Sciences, Dinoflagellida, Original Article, Evolutionary ecology, Metagenomics
Abstract: International audience; Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). Phylogenetic analyses of the endosymbionts based on the 28S rDNA gene revealed multiple novel closely related Symbiodinium clade A genotypes. A haplotype network using the high-resolution internal transcribed spacer-2 marker showed that these genotypes form eight divergent, biogeographically structured, subclade types that do not seem to associate with any benthic hosts. Ecological analyses using the Tara Oceans metabarcoding data set (V9 region of the 18S rDNA) and contextual oceanographic parameters showed a global distribution of the symbiotic partnership in nutrient-poor surface waters. The discovery of the symbiotic life of Symbiodinium in the open ocean provides new insights into the ecology and evolution of this pivotal microalga and raises new hypotheses about coastal pelagic connectivity.
Published: 2015
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3. Deep sequencing of amplifiedPrasinovirusand host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

Author: Sarah Romac, Stéphane Audic, Julie Poulain, Camille Clerissi, Patrick Wincker, Raffaella Casotti, Colomban de Vargas, Hiroyuki Ogata, Nigel Grimsley, Yves Desdevises, Silvia G. Acinas, and Pascal Hingamp
Subjects: 0303 health sciences, food.ingredient, biology, 030306 microbiology, Ecology, Host (biology), biology.organism_classification, Prasinovirus, Agricultural and Biological Sciences (miscellaneous), Deep sequencing, Bathycoccus, Ostreococcus, 03 medical and health sciences, food, 14. Life underwater, Species richness, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Trophic level, Micromonas
Abstract: High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey–predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.
Published: 2015
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4. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Author: Bente Edvardsen, Sarah Romac, Richard Christen, Colomban de Vargas, Thorsten Stoeck, Jean-Michel Claverie, Ramon Massana, Ian Probert, Johan Decelle, Laure Guillou, David Bass, Wiebe H. C. F. Kooistra, Nathalie Simon, Jan Pawlowski, Raffaele Siano, Ramiro Logares, Micah Dunthorn, Sébastien Santini, Adriana Zingone, Aurélie Chambouvet, Stéphane Audic, John R. Dolan, Hiroyuki Ogata, Christophe Boutte, Fabrice Not, Irene Forn, Lucie Bittner, Thomas A. Richards, Frédéric Mahé, Kamran Shalchian-Tabrizi, Massimo C. Pernice, Dominik Forster, Olivier Jaillon, Daniel Vaulot, and Angélique Gobet
Subjects: biology, Ecology, fungi, Protist, 15. Life on land, biology.organism_classification, medicine.disease_cause, Microbiology, DNA sequencing, medicine, Acantharia, Pyrosequencing, Marine ecosystem, 14. Life underwater, Picoplankton, Ribosomal DNA, Ecology, Evolution, Behavior and Systematics, Dinophyceae
Abstract: Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
Published: 2015
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5. PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution

Author: Michael Siccha, Gilles Escarguel, Christophe J. Douady, Frédéric Quillévéré, Stéphane Audic, Thibault de Garidel-Thoron, Frédéric Mahé, Agnes K. M. Weiner, Christopher M. Wade, Colomban de Vargas, Heidi A. Seears, Raphael Morard, Michal Kucera, Aurore André, Yurika Ujiié, and Kate F. Darling
Subjects: 010506 paleontology, 0303 health sciences, biology, Database, Sequence database, Ecology, Biogeography, fungi, Rhizaria, biology.organism_classification, computer.software_genre, 01 natural sciences, Molecular ecology, Foraminifera, 03 medical and health sciences, Taxon, Genetics, Identification (biology), 14. Life underwater, Ribosomal DNA, computer, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0105 earth and related environmental sciences, Biotechnology
Abstract: Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR2, the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR2 website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.
Published: 2015
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6. Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

Author: Julie Poulain, Stephane Pesant, Fabrice Not, Stéphane Audic, Andrés Gutiérrez-Rodríguez, Estelle Bigeard, Lars Stemmann, Tristan Biard, 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Génomique métabolique (UMR 8030), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), National Institute of Water and Atmospheric Research [Wellington] (NIWA), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Biogeography, Oceans and Seas, Biome, Microbiology, DNA, Ribosomal, 03 medical and health sciences, RNA, Ribosomal, 18S, Animals, 14. Life underwater, Ribosomal DNA, Ecology, Evolution, Behavior and Systematics, Phylogeny, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Trophic level, biology, Ecology, fungi, Rhizaria, Genetic Variation, Plankton, biology.organism_classification, 030104 developmental biology, Environmental biotechnology, Original Article, Animal Distribution, human activities, Radiolaria
Abstract: Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770 +/- 1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474 +/- 17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.
Published: 2017
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7. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms

Author: Colomban de Vargas, Daniel Vaulot, Stéphane Audic, Shinya Yoshikawa, Mary-Hélène Noël, Akira Kuwata, Mitsunobu Kamiya, Priscillia Gourvil, Adriana Lopes dos Santos, Kaori Ohki, Mutsuo Ichinomiya, Prefectural University of Kumamoto, 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), Fukui Prefectural University, University of Fukui, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), National Institute for Environmental Studies (NIES), Tohoku National Fisheries Research Institute, and National Fisheries Research Institute
Subjects: 0301 basic medicine, Operational taxonomic unit, Bolidomonas, Oceans and Seas, Molecular Sequence Data, Antarctic Regions, DNA, Ribosomal, Microbiology, rail, 03 medical and health sciences, Monophyly, Mediterranean sea, Algae, Mediterranean Sea, Seawater, 14. Life underwater, Clade, Phylogeny, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Diatoms, biology, Ecology, rail.locomotive_class, Biodiversity, biology.organism_classification, 030104 developmental biology, Phytoplankton, Bolidophyceae, Original Article, Taxonomy (biology)
Abstract: International audience; Bolidomonas is a genus of picoplanktonic flagellated algae that is closely related to diatoms. Triparma laevis, a species belonging to the Parmales, which are small cells with a siliceous covering, has been shown to form a monophyletic group with Bolidomonas. We isolated several novel strains of Bolidophyceae that have permitted further exploration of the diversity of this group using nuclear, plastidial and mitochondrial genes. The resulting phylogenetic data led us to formally emend the taxonomy of this group to include the Parmales within the Bolidophyceae, to combine Bolidomonas within Triparma and to define a novel species, Triparma eleuthera sp. nov. The global distribution of Bolidophyceae was then assessed using environmental sequences available in public databases, as well as a large 18S rRNA V9 metabarcode data set from the Tara Oceans expedition. Bolidophyceans appear ubiquitous throughout the sampled oceans but always constitute a minor component of the phytoplankton community, corresponding to at most ~ 4% of the metabarcodes from photosynthetic groups (excluding dinoflagellates). They are ~ 10 times more abundant in the small size fraction (0.8– 5 μm) than in larger size fractions. T. eleuthera sp. nov. constitutes the most abundant and most widespread operational taxonomic unit (OTU) followed by T. pacifica, T. mediterranea and the T. laevis clade. The T. mediterranea OTU is characteristic of Mediterranean Sea surface waters and the T. laevis clade OTU is most prevalent in colder waters, in particular off Antarctica.
Published: 2016
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8. Insights into global diatom distribution and diversity in the world's ocean

Author: Daniele Iudicone, Stéphane Audic, Colomban de Vargas, Patrick Wincker, Flora Vincent, Chris Bowler, Shruti Malviya, Julie Poulain, Alaguraj Veluchamy, Eleonora Scalco, Adriana Zingone, Lucie Bittner, Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Ministero dell'Istruzione dell'Universit a e della Ricerca RITMARE project, Centre National de la Recherche Scientifique, Agnes b., Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, Electricite de France (EDF) Foundation EDF Diversiterre, Fondation pour la Recherche sur la Biodiversite, Prince Albert II de Monaco Foundation, Etienne Bourgois, Groupement de Recherche [GDR3280], Tara schooner, European Molecular Biology Laboratory, Genoscope/Commissariat a l'Energie Atomique, French Government ``Investissements d'Avenir' [ANR-11-BTBR-0008, ANR-10-INBS-09-08, ANR-10-LABX-54], Paris Sciences et Lettres (PSLstar) Research University [ANR-11-IDEX-0001-02], Agence Nationale de la Recherche (ANR) [ANR-10-INBS-09-08, ANR-09-BLAN-0348, ANR-09-GENM-031, ANR-2010-1709-01], European Union [287589], European Research Council [294823], Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Aquatic Organisms, Databases, Factual, Range (biology), Oceans and Seas, Biodiversity, Tara Oceans, DNA, Ribosomal, 01 natural sciences, diatoms, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Phytoplankton, Photic zone, 14. Life underwater, Ecosystem, biodiversity, Microscopy, Multidisciplinary, biology, choke points, Ecology, 010604 marine biology & hydrobiology, Ocean current, Reproducibility of Results, Chaetoceros, Plankton, biology.organism_classification, 030104 developmental biology, Oceanography, Diatom, PNAS Plus, metabarcoding
Abstract: International audience; Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of similar to 12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.
Published: 2016
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9. A role for diatom-like silicon transporters in calcifying coccolithophores

Author: Colomban de Vargas, Stéphane Audic, Alison Taylor, Charlotte E. Walker, Ian Probert, Declan C. Schroeder, Grażyna M. Durak, Glen L. Wheeler, and Colin Brownlee
Subjects: 0301 basic medicine, Silicon, Coccolithophore, Science, General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, Article, Haptophyte, 03 medical and health sciences, Calcification, Physiologic, Phytoplankton, Seawater, 14. Life underwater, Emiliania huxleyi, Diatoms, Multidisciplinary, biology, Ecology, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, fungi, technology, industry, and agriculture, Haptophyta, Membrane Transport Proteins, General Chemistry, biology.organism_classification, Microscopy, Electron, 030104 developmental biology, Diatom, Microscopy, Fluorescence, ddc:540, Electrophoresis, Polyacrylamide Gel, Biomineralization
Abstract: Biomineralization by marine phytoplankton, such as the silicifying diatoms and calcifying coccolithophores, plays an important role in carbon and nutrient cycling in the oceans. Silicification and calcification are distinct cellular processes with no known common mechanisms. It is thought that coccolithophores are able to outcompete diatoms in Si-depleted waters, which can contribute to the formation of coccolithophore blooms. Here we show that an expanded family of diatom-like silicon transporters (SITs) are present in both silicifying and calcifying haptophyte phytoplankton, including some globally important coccolithophores. Si is required for calcification in these coccolithophores, indicating that Si uptake contributes to the very different forms of biomineralization in diatoms and coccolithophores. Significantly, SITs and the requirement for Si are absent from highly abundant bloom-forming coccolithophores, such as Emiliania huxleyi. These very different requirements for Si in coccolithophores are likely to have major influence on their competitive interactions with diatoms and other siliceous phytoplankton., Silicification by diatoms and calcification by coccolithophores are distinct biomineralisation processes that influence global carbon cycling and the abundance of marine plankton. Here, Durak et al. show that diatom-like silicon transporters are present in coccolithophores, and that silicon is required for formation of their calcium carbonate coccoliths.
Published: 2016

10. Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

Author: Bente Edvardsen, Ian Probert, Hiroyuki Ogata, Colomban de Vargas, Sébastien Santini, Angélique Gobet, Lucie Bittner, Stéphane Audic, Sarah Romac, Elianne Egge, 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), Max Planck Institute for Biological Cybernetics, Max-Planck-Gesellschaft, Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: DNA Primers, 0106 biological sciences, MESH: Sequence Analysis, DNA, MESH: Mediterranean Sea, MESH: Genetics, Population, Haptophyta, DNA, Ribosomal, 010603 evolutionary biology, 01 natural sciences, Haptophyte, 03 medical and health sciences, symbols.namesake, Botany, Mediterranean Sea, MESH: Plankton, Genetics, MESH: Genetic Variation, 14. Life underwater, MESH: Phylogeny, Ribosomal DNA, Phylogeny, Ecology, Evolution, Behavior and Systematics, DNA Primers, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Sanger sequencing, 0303 health sciences, Deep chlorophyll maximum, Genetic diversity, MESH: DNA, Ribosomal, biology, Phylum, Genetic Variation, MESH: Italy, Sequence Analysis, DNA, Plankton, biology.organism_classification, Genetics, Population, Bays, Italy, Evolutionary biology, MESH: Bays, symbols, Pyrosequencing, MESH: Haptophyta
Abstract: International audience; Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size-fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8-3 or 3-20 μm) and two sampling depths [subsurface, at 1 m, or deep chlorophyll maximum (DCM) at 23 m]. 454 reads were identified using a database covering the entire Haptophyta diversity currently sequenced. Our data set revealed several hundreds of Haptophyte clusters. However, most of these clusters could not be linked to taxonomically known sequences: considering OTUs(97%) (clusters build at a sequence identity level of 97%) on our global data set, less than 1% of the reads clustered with sequences from cultures, and less than 12% clustered with reference sequences obtained previously from cloning and Sanger sequencing of environmental samples. Thus, we highlighted a large uncharacterized environmental genetic diversity, which clearly shows that currently cultivated species poorly reflect the actual diversity present in the natural environment. Haptophyte community appeared to be significantly structured according to the depth. The highest diversity and evenness were obtained in samples from the DCM, and samples from the large size fraction (3-20 μm) taken at the DCM shared a lower proportion of common OTUs(97%) with the other samples. Reads from the species Chrysoculter romboideus were notably found at the DCM, while they could be detected at the subsurface. The highest proportion of totally unknown OTUs(97%) was collected at the DCM in the smallest size fraction (0.8-3 μm). Overall, this study emphasized several technical and theoretical barriers inherent to the exploration of the large and largely unknown diversity of unicellular eukaryotes.
Published: 2012
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11. Gene Expression in Proliferating Cells of the Dinoflagellate Alexandrium catenella (Dinophyceae)

Author: Stéphane Audic, Guillaume Blanc, Eve Toulza, Yves Collos, Mohamed Laabir, Daniel Grzebyk, Jean-Michel Claverie, and Mi-Sun Shin
Subjects: Alexandrium catenella, Genes, Protozoan, Protozoan Proteins, Genetics and Molecular Biology, Biology, medicine.disease_cause, Applied Microbiology and Biotechnology, Gene expression, medicine, Photosynthesis, Gene, Cell Proliferation, Gene Library, Regulation of gene expression, Ecology, Toxin, Cell growth, Dinoflagellate, Computational Biology, Sequence Analysis, DNA, Cell cycle, biology.organism_classification, Molecular biology, Cell biology, Gene Expression Regulation, Dinoflagellida, RNA, Protozoan, Food Science, Biotechnology
Abstract: Understanding the conditions leading to harmful algal blooms, especially those produced by toxic dinoflagellate species, is important for environmental and health safety. In addition to investigations into the environmental conditions necessary for the formation of toxic blooms, we postulate that investigating gene expression in proliferating cells is essential for understanding bloom dynamics. Expressed sequence tags were produced from cultured cells of the toxic dinoflagellate Alexandrium catenella sampled during the initiation phase of growth using Sanger's method and by 454 pyrosequencing. A significant proportion of identified genes (ca. 25%) represented enzymes and proteins that participate in a variety of cellular regulatory mechanisms that may characterize proliferating cells, e.g., control of the cell cycle and division, regulation of transcription, translation and posttranslational protein modifications, signaling, intracellular trafficking, and transport. All of the several genes selected for gene expression assays due to their involvement in metabolism and the cell cycle were overexpressed during exponential growth. These data will be useful for investigating the mechanisms underlying growth and toxin production in toxic Alexandrium species and for studying and monitoring the development of toxic blooms.
Published: 2010
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12. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus

Author: Matthieu Legendre, Alain Bernadac, Pascal Hingamp, Chantal Abergel, Stéphane Audic, Olivier Poirot, Julie Poulain, Audrey Lartigue, Magali Lescot, Deborah Byrne, Jean-Michel Claverie, Virginie Seltzer, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale et microbiologie (IBSM), Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and ANR-08-BLAN-0089,MIMIVIRUS,Etude de la relation hôte pathogène du système Acanthamoeba/Mimivirus(2008)
Subjects: Gene Expression Regulation, Viral, DNA, Complementary, Genes, Viral, [SDV]Life Sciences [q-bio], Acanthamoeba, Genome, Viral, Nucleocytoplasmic large DNA viruses, Viral Proteins, Genetics, Animals, Mimiviridae, Giant Virus, RNA, Messenger, Genetics (clinical), Mimivirus, biology, Pandoravirus, Gene Expression Profiling, Research, Virophage, Virion, Sequence Analysis, DNA, biology.organism_classification, Microscopy, Electron, MRNA Sequencing, RNA, Viral, Megavirus
Abstract: Mimivirus, a virus infecting Acanthamoeba, is the prototype of the Mimiviridae, the latest addition to the nucleocytoplasmic large DNA viruses. The Mimivirus genome encodes close to 1000 proteins, many of them never before encountered in a virus, such as four amino-acyl tRNA synthetases. To explore the physiology of this exceptional virus and identify the genes involved in the building of its characteristic intracytoplasmic “virion factory,” we coupled electron microscopy observations with the massively parallel pyrosequencing of the polyadenylated RNA fractions of Acanthamoeba castellanii cells at various time post-infection. We generated 633,346 reads, of which 322,904 correspond to Mimivirus transcripts. This first application of deep mRNA sequencing (454 Life Sciences [Roche] FLX) to a large DNA virus allowed the precise delineation of the 5′ and 3′ extremities of Mimivirus mRNAs and revealed 75 new transcripts including several noncoding RNAs. Mimivirus genes are expressed across a wide dynamic range, in a finely regulated manner broadly described by three main temporal classes: early, intermediate, and late. This RNA-seq study confirmed the AAAATTGA sequence as an early promoter element, as well as the presence of palindromes at most of the polyadenylation sites. It also revealed a new promoter element correlating with late gene expression, which is also prominent in Sputnik, the recently described Mimivirus “virophage.” These results—validated genome-wide by the hybridization of total RNA extracted from infected Acanthamoeba cells on a tiling array (Agilent)—will constitute the foundation on which to build subsequent functional studies of the Mimivirus/Acanthamoeba system.
Published: 2010
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13. The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates

Author: Stéphane Audic, Anna Gimmler, Ralf Korn, Colomban de Vargas, Thorsten Stoeck, Publica, University of Kaiserslautern [Kaiserslautern], Fraunhofer Institute of Industrial Mathematics (Fraunhofer ITWM), Fraunhofer (Fraunhofer-Gesellschaft), 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: Chlorophyll, 0106 biological sciences, 0301 basic medicine, Aquatic Organisms, Internationality, Oceans and Seas, Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, Statistics, Nonparametric, Article, Latitude, 03 medical and health sciences, 14. Life underwater, Taxonomic rank, Ciliate, Deep chlorophyll maximum, Multidisciplinary, Geography, Ecology, Genetic Variation, Pelagic zone, Plankton, biology.organism_classification, 030104 developmental biology, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Illumina reads of the SSU-rDNA-V9 region obtained from the circumglobal Tara Oceans expedition allow the investigation of protistan plankton diversity patterns on a global scale. We analyzed 6,137,350 V9-amplicons from ocean surface waters and the deep chlorophyll maximum, which were taxonomically assigned to the phylum Ciliophora. For open ocean samples global planktonic ciliate diversity is relatively low (ca. 1,300 observed and predicted ciliate OTUs). We found that 17% of all detected ciliate OTUs occurred in all oceanic regions under study. On average, local ciliate OTU richness represented 27% of the global ciliate OTU richness, indicating that a large proportion of ciliates is widely distributed. Yet, more than half of these OTUs shared Tara Oceans dataset did not reveal any evidence that latitude is structuring ciliate communities.
Published: 2016
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14. Benthic protists: the under-charted majority

Author: Diana Sarno, Nathalie Simon, John R. Dolan, Adriana Zingone, Patrick Wincker, Jan Pawlowski, Wiebe H. C. F. Kooistra, Bente Edvardsen, Marina Montresor, Fabrice Not, Colomban de Vargas, Thorsten Stoeck, Ramiro Logares, Elianne Egge, Sarah Romac, Stéphane Audic, Thomas A. Richards, Micah Dunthorn, Wenche Eikrem, Ramon Massana, Johan Decelle, Richard Christen, Hiroyuki Ogata, Dominik Forster, Kamran Shalchian-Tabrizi, Massimo C. Pernice, Raffaele Siano, Lucie Bittner, Jean-Michel Claverie, Frédéric Mahé, Daniel Vaulot, Angélique Gobet, David Bass, Christophe Boutte, Sébastien Santini, University of Kaiserslautern [Kaiserslautern], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), 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), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (Cefas), Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Symbiose Marine (SM), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Oslo (UiO), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Stazione Zoologica Anton Dohrn (SZN), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Diversité et Interactions au sein du Plancton Océanique (DIPO), Kyoto University [Kyoto], Department of Genetics and Evolution [Genève], University of Geneva [Switzerland], University of Exeter, Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), Stipendienstiftung Rheinland-Pfalz, European Commission, German Research Foundation, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, Université de Genève = University of Geneva (UNIGE), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of ecology, Universität Kaiserslautern, Microbial Ecology, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie virtuelle, COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), Max Planck Institute for Biological Cybernetics, Max-Planck-Gesellschaft, Marine Botany, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Department of genetics and evolution, School of Geography and Environmental, Monash University, Monash University [Clayton], Dynamiques de l'Environnement Côtier (DYNECO), Commissariat à l'Energie Atomique, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0106 biological sciences, 0301 basic medicine, Aquatic Organisms, Geologic Sediments, Foraminifera, medicine.disease_cause, 01 natural sciences, Applied Microbiology and Biotechnology, 18S ribosomal RNA, Benthic microbial communities, Sequence Read Archive, Phylogeny, High-throughput sequencing, Ecology, Protist, high-throughput sequencing, Biodiversity, Plankton, respiratory system, protist diversity, Benthic zone, geographic locations, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Microbiology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Hydrothermal Vents, benthic microbial communities, coastal environments, parasitic diseases, RNA, Ribosomal, 18S, medicine, 14. Life underwater, Ecosystem, Diatoms, Base Sequence, 010604 marine biology & hydrobiology, fungi, DNA, Sequence Analysis, DNA, 030104 developmental biology, Taxon, Protist diversity, Reference database, Coastal environments, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities
Abstract: Forster, Dominik ... et al.-- 11 pages, 6 figures, 1 table, supplementary data http://femsec.oxfordjournals.org/content/suppl/2016/06/05/fiw120.DC1, Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed, This work was supported by the European Commission and is part of the EU-FP7 ERA-net program BiodivERsA, under the project BioMarKs [2008-6530]. Dominik Forster was supported by a graduate scholarship of Stipendienstiftung Rheinland-Pfalz. Micah Dunthorn and Frédéric Mahé were supported by the Deutsche Forschungsgemeinschaft [grant #DU1319/1-1]. Thorsten Stoeck was supported by the Deutsche Forschungsgemeinschaft [grant #STO414/11-1]. Daniel Vaulot was supported by the European Union [grants MicroB3/FP7-287589, MaCuMBA/FP7-KBBE-2012-6-311975]
Published: 2016
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15. Global distribution and vertical patterns of a prymnesiophyte-cyanobacteria obligate symbiosis

Author: Montserrat Vidal, Ramon Massana, Stéphane Audic, Mikel Latasa, Francisco M. Cornejo-Castillo, Silvia G. Acinas, Nicolás Raho, Colomban de Vargas, Dolors Blasco, Ana María Cabello, Ministerio de Economía y Competitividad (España), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of molecular Biology, Universidad Autonoma de Madrid (UAM), Department of Ecology, University of Barcelona, 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), Centro Oceanográfico de Gijón (IEO), and Universidad Autónoma de Madrid (UAM)
Subjects: 0301 basic medicine, Cyanobacteria, Oceans and Seas, Biology, Microbiology, 03 medical and health sciences, Symbiosis, Abundance (ecology), Phylogenetics, Nitrogen Fixation, Seawater, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Medio Marino, Relative species abundance, In Situ Hybridization, Fluorescence, Phylogeny, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Centro Oceanográfico de Gijón, Deep chlorophyll maximum, Obligate, Geomicrobiology, Ecology, Haptophyta, biology.organism_classification, 030104 developmental biology, Original Article
Abstract: 14 pages, 6 figures, 1 table, A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small prymnesiophyte and the clade UCYN-A2 in symbiosis with the larger Braarudosphaera bigelowii. We targeted the prymnesiophyte–UCYN-A1 symbiosis by double CARD-FISH (catalyzed reporter deposition-fluorescence in situ hybridization) and analyzed its abundance in surface samples from the MALASPINA circumnavigation expedition. Our use of a specific probe for the prymnesiophyte partner allowed us to verify that this algal species virtually always carried the UCYN-A symbiont, indicating that the association was also obligate for the host. The prymnesiophyte–UCYN-A1 symbiosis was detected in all ocean basins, displaying a patchy distribution with abundances (up to 500 cells ml− 1) that could vary orders of magnitude. Additional vertical profiles taken at the NE Atlantic showed that this symbiosis occupied the upper water column and disappeared towards the Deep Chlorophyll Maximum, where the biomass of the prymnesiophyte assemblage peaked. Moreover, sequences of both prymnesiophyte partners were searched within a large 18S rDNA metabarcoding data set from the Tara-Oceans expedition around the world. This sequence-based analysis supported the patchy distribution of the UCYN-A1 host observed by CARD-FISH and highlighted an unexpected homogeneous distribution (at low relative abundance) of B. bigelowii in the open ocean. Our results demonstrate that partners are always in symbiosis in nature and show contrasted ecological patterns of the two related lineages, Financial support has been provided by the Spanish Ministry of Economy and Competitivity through project Consolider-Ingenio Malaspina 2010 (CSD2008-00077) to CMD, FLAME (CGL2010-16304) to RM, and PANGENOMICS (CGL2011-26848/BOS) to SGA. AMC was recipient of a Spanish FPI grant (BES-2009-027194)
Published: 2016
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16. Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome

Author: Jean-Michel Claverie, Guillaume Blanc, Didier Raoult, Catherine Robert, Stéphane Audic, and Hiroyuki Ogata
Subjects: Rickettsia massiliae, Genetics, Letter, Gene Transfer, Horizontal, biology, Obligate, Rickettsia Infections, bacterial infections and mycoses, biology.organism_classification, Genome, Spotted fever, Plasmid, Rickettsia, Genes, Bacterial, Multigene Family, Horizontal gene transfer, bacteria, Gene, Genome, Bacterial, Phylogeny, Genetics (clinical)
Abstract: Rickettsia massiliae is a tick-borne obligate intracellular α-proteobacteria causing spotted fever in humans. Here, we present the sequence of its genome, comprising a 1.3-Mb circular chromosome and a 15.3-kb plasmid. The chromosome exhibits long-range colinearity with the other Spotted Fever Group Rickettsia genomes, except for a large fragment specific to R. massiliae that contains 14 tra genes presumably involved in pilus formation and conjugal DNA transfer. We demonstrate that the tra region was acquired recently by lateral gene transfer (LGT) from a species related to Rickettsia bellii. Further analysis of the genomic sequences identifies additional candidates of LGT between Rickettsia. Our study indicates that recent LGT between obligate intracellular Rickettsia is more common than previously thought.
Published: 2007
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17. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

Author: Colomban, de Vargas, Stéphane, Audic, Nicolas, Henry, Johan, Decelle, Frédéric, Mahé, Ramiro, Logares, Enrique, Lara, Cédric, Berney, Noan, Le Bescot, Ian, Probert, Margaux, Carmichael, Julie, Poulain, Sarah, Romac, Sébastien, Colin, Jean-Marc, Aury, Lucie, Bittner, Samuel, Chaffron, Micah, Dunthorn, Stefan, Engelen, Olga, Flegontova, Lionel, Guidi, Aleš, Horák, Olivier, Jaillon, Gipsi, Lima-Mendez, Julius, Lukeš, Shruti, Malviya, Raphael, Morard, Matthieu, Mulot, Eleonora, Scalco, Raffaele, Siano, Flora, Vincent, Adriana, Zingone, Céline, Dimier, Marc, Picheral, Sarah, Searson, Stefanie, Kandels-Lewis, Silvia G, Acinas, Peer, Bork, Chris, Bowler, Gabriel, Gorsky, Nigel, Grimsley, Pascal, Hingamp, Daniele, Iudicone, Fabrice, Not, Hiroyuki, Ogata, Stephane, Pesant, Jeroen, Raes, Michael E, Sieracki, Sabrina, Speich, Lars, Stemmann, Shinichi, Sunagawa, Jean, Weissenbach, and Patrick, Wincker
Subjects: Oceans and Seas, Sunlight, Animals, DNA Barcoding, Taxonomic, Eukaryota, Biodiversity, Sequence Analysis, DNA, Plankton, DNA, Ribosomal, Ribosomes, Phylogeny
Abstract: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists,0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.
Published: 2015

18. Ocean plankton. Determinants of community structure in the global plankton interactome

Author: Gipsi, Lima-Mendez, Karoline, Faust, Nicolas, Henry, Johan, Decelle, Sébastien, Colin, Fabrizio, Carcillo, Samuel, Chaffron, J Cesar, Ignacio-Espinosa, Simon, Roux, Flora, Vincent, Lucie, Bittner, Youssef, Darzi, Jun, Wang, Stéphane, Audic, Léo, Berline, Gianluca, Bontempi, Ana M, Cabello, Laurent, Coppola, Francisco M, Cornejo-Castillo, Francesco, d'Ovidio, Luc, De Meester, Isabel, Ferrera, Marie-José, Garet-Delmas, Lionel, Guidi, Elena, Lara, Stéphane, Pesant, Marta, Royo-Llonch, Guillem, Salazar, Pablo, Sánchez, Marta, Sebastian, Caroline, Souffreau, Céline, Dimier, Marc, Picheral, Sarah, Searson, Stefanie, Kandels-Lewis, Gabriel, Gorsky, Fabrice, Not, Hiroyuki, Ogata, Sabrina, Speich, Lars, Stemmann, Jean, Weissenbach, Patrick, Wincker, Silvia G, Acinas, Shinichi, Sunagawa, Peer, Bork, Matthew B, Sullivan, Eric, Karsenti, Chris, Bowler, and Colomban, de Vargas
Subjects: Food Chain, Platyhelminths, Oceans and Seas, Viruses, Sunlight, Animals, Plankton, Symbiosis, Host Specificity, Phylogeny
Abstract: Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.
Published: 2015

19. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author: Colomban de Vargas, Stefanie Kandels-Lewis, Gregory K. Farrant, Laurence Garczarek, Hiroyuki Ogata, Silvia G. Acinas, Pascal Hingamp, Shruti Malviya, Lucie Bittner, Bruno Blanke, Matthew B. Sullivan, Michael J. Follows, Sarah Searson, Patrick Wincker, Oliver Jahn, Emilie Villar, Cyrille Lepoivre, Jennifer R. Brum, Shinichi Sunagawa, Thomas Vannier, Lionel Guidi, Pierre Testor, Tara Oceans Coordinators, Hervé Le Goff, Chris Hill, Daniele Iudicone, Stéphane Audic, Sébastien Santini, Stephane Pesant, Adriana Zingone, Gabriel Gorsky, Fabrice Not, Nicolas Grima, Jean-Baptiste Romagnan, Céline Dimier, Atsuko Tanaka, Raffaella Casotti, Jean-Pierre Gattuso, Flora Vincent, John R. Dolan, Eric Pelletier, Alison Chase, Jean-Louis Jamet, Emmanuel Boss, Eleonora Scalco, Fabrizio D'Ortenzio, Peer Bork, Christophe Brunet, Marc Picheral, Sabrina Speich, Simon Roux, Chris Bowler, Eric Karsenti, Sarah M. Schwenck, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Massachusetts Institute of Technology (MIT), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut de biologie de l'ENS Paris (IBENS), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Arizona, Stazione Zoologica Anton Dohrn (SZN), University of Maine, Observatoire océanologique de Villefranche-sur-mer (OOVM), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Processus de Transfert et d'Echanges dans l'Environnement - EA 3819 (PROTEE), Université de Toulon (UTLN), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Développement Instrumental et Techniques Marines (DITM), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Variabilité de l'Océan et de la Glace de mer (VOG), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Heidelberg] (EMBL), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Max Delbrück Centre for Molecular Medicine, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, We appreciate the commitment of the following people and sponsors: CNRS (in particular, Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Fund for Scientific Research–Flanders, Rega Institute, KU Leuven, the French Ministry of Research, the French government Investissements d’Avenir programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), and ANR (projects POSEIDON/ ANR-09-BLAN- 0348, PHYTBACK/ANR-2010-1709-01, PROMETHEUS/ANR-09-PCS-GENM-217, SAMOSA/ANR-13-ADAP0010, and TARAGIRUS/ANR-09-PCS-GENM-218), European Union FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376, and MaCuMBA/No.311975), ERC Advanced Grant Award to C.B. (Diatomite: 294823), Gordon and Betty Moore Foundation grant (no. 3790) to M.B.S., Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to S.G.A., TANIT (CONES 2010-0036) from the Agència de Gestió d´Ajusts Universitaris i Reserca to S.G.A., JSPS KAKENHI grant no. 26430184 to H.O., NASA Ocean Biology and Biogeochemistry program (NNX11AQ14G and NNX09AU43G) to E.B., The Italian Research for the Sea (Flagship Project RITMARE) to D.I., and FWO, BIO5, and Biosphere 2 to M.B.S. We also appreciate the support and commitment of Agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the EDF Foundation, FRB, the Prince Albert II de Monaco Foundation, and the Tara schooner and its captains and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that graciously granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org). We also acknowledge excellent assistance from the European Bioinformatics Institute (EBI), in particular G. Cochrane and P. ten Hoopen, as well as the EMBL Advanced Light Microscopy Facility (ALMF), in particular R. Pepperkok. We thank Y. Timsit for stimulating scientific discussions and critical help during writing of the manuscript. The altimeter products were produced by Ssalto/Duacs and CLS, with support from CNES., ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-09-BLAN-0348,POSEIDON(2009), ANR-10-BLAN-1709,PHYTBACK,Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton(2010), ANR-13-ADAP-0010,SAMOSA,Synechococcus as a model genus for studying adaptation of marine phytoplankton to environmental changes(2013), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), European Project: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Institut de biologie de l'ENS Paris (UMR 8197/1024) (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)-École normale supérieure - Paris (ENS Paris), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, 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)
Subjects: 0303 health sciences, Atlantic hurricane, Biogeochemical cycle, Multidisciplinary, 010504 meteorology & atmospheric sciences, Ocean current, fungi, Biology, Plankton, 01 natural sciences, 03 medical and health sciences, Indian ocean, Oceanography, Biological dispersal, Seawater, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Nitrogen cycle, 030304 developmental biology, 0105 earth and related environmental sciences
Abstract: Villar, Emilie ... et. al.-- 11 pages, 8 figures, supplementary materials www.sciencemag.org/content/348/6237/1261447/suppl/DC1, Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic. © 2015, American Association for the Advancement of Science. All rights reserved, We appreciate the commitment of the following people and sponsors: CNRS (in particular, Groupement de Recherche GDR3280); European Molecular Biology Laboratory (EMBL); Genoscope/CEA; VIB; Stazione Zoologica Anton Dohrn; UNIMIB; Fund for Scientific Research–Flanders; Rega Institute, KU Leuven; the French Ministry of Research; the French government Investissements d’Avenir programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), and ANR (projects POSEIDON/ ANR-09-BLAN- 0348, PHYTBACK/ANR-2010-1709-01, PROMETHEUS/ANR-09-PCS-GENM-217, SAMOSA/ANR-13-ADAP-0010, and TARAGIRUS/ANR-09-PCS-GENM-218); European Union FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376, and MaCuMBA/No.311975); ERC Advanced Grant Award to C.B. (Diatomite: 294823); Gordon and Betty Moore Foundation grant (no. 3790) to M.B.S.; Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to S.G.A.; TANIT (CONES 2010-0036) from the Agència de Gestió d´Ajusts Universitaris i Reserca to S.G.A.; JSPS KAKENHI grant no. 26430184 to H.O.; NASA Ocean Biology and Biogeochemistry program (NNX11AQ14G and NNX09AU43G) to E.B.; The Italian Research for the Sea (Flagship Project RITMARE) to D.I.; and FWO, BIO5, and Biosphere 2 to M.B.S.We also appreciate the support and commitment of Agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the EDF Foundation, FRB, the Prince Albert II de Monaco Foundation, and the Tara schooner and its captains and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that graciously granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015
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20. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author: Emilie, Villar, Gregory K, Farrant, Michael, Follows, Laurence, Garczarek, Sabrina, Speich, Stéphane, Audic, Lucie, Bittner, Bruno, Blanke, Jennifer R, Brum, Christophe, Brunet, Raffaella, Casotti, Alison, Chase, John R, Dolan, Fabrizio, d'Ortenzio, Jean-Pierre, Gattuso, Nicolas, Grima, Lionel, Guidi, Christopher N, Hill, Oliver, Jahn, Jean-Louis, Jamet, Hervé, Le Goff, Cyrille, Lepoivre, Shruti, Malviya, Eric, Pelletier, Jean-Baptiste, Romagnan, Simon, Roux, Sébastien, Santini, Eleonora, Scalco, Sarah M, Schwenck, Atsuko, Tanaka, Pierre, Testor, Thomas, Vannier, Flora, Vincent, Adriana, Zingone, Céline, Dimier, Marc, Picheral, Sarah, Searson, Stefanie, Kandels-Lewis, Silvia G, Acinas, Peer, Bork, Emmanuel, Boss, Colomban, de Vargas, Gabriel, Gorsky, Hiroyuki, Ogata, Stéphane, Pesant, Matthew B, Sullivan, Shinichi, Sunagawa, Patrick, Wincker, Eric, Karsenti, Chris, Bowler, Fabrice, Not, Pascal, Hingamp, and Raes, Jeroen
Subjects: Nitrogen, fungi, Genetic Variation, Seawater, Metagenomics, Selection, Genetic, Plankton, Atlantic Ocean, DNA, Ribosomal, Indian Ocean, Nitrites
Abstract: Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic. ispartof: Science vol:348 issue:6237 ispartof: location:United States status: published
Published: 2015

21. MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution

Author: Stéphane Audic, Christian Jeanthon, Loraine Brillet-Guéguen, Christophe Caron, Dominique Boeuf, 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), 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), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-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)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Agence Nationale de la Recherche [ANR 11 BSV7 021 02], European Union [287589], ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), and MArine Phototrophic Prokaryotes (MAPP)
Subjects: [SDV]Life Sciences [q-bio], Sequence alignment, computer.software_genre, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Three-domain system, RNA, Ribosomal, 16S, RNA RIBOSOMAL 16S, Phylogeny, 030304 developmental biology, 0303 health sciences, Database, biology, Phylogenetic tree, 030306 microbiology, Microbial rhodopsin, Metadata, Rhodopsin, Bacteriorhodopsins, [SDE]Environmental Sciences, biology.protein, Original Article, General Agricultural and Biological Sciences, Databases, Nucleic Acid, computer, Sequence Alignment, Information Systems
Abstract: Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr.
Published: 2015
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22. Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

Author: Eric Bapteste, Slim Karkar, Sarah Romac, Thorsten Stoeck, Lucie Bittner, Philippe Lopez, Micah Dunthorn, Stéphane Audic, Dominik Forster, Department of ecology, Universität Kaiserslautern, Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), and Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Microbial diversity, Physiology, Plant Science, medicine.disease_cause, 01 natural sciences, Structural Biology, Databases, Genetic, Gene Regulatory Networks, Sanger sequencing, 0303 health sciences, High-throughput sequencing, Geography, Agricultural and Biological Sciences(all), Ecology, Protist, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biogeography, symbols, General Agricultural and Biological Sciences, Research Article, Biotechnology, DNA, Complementary, Ecology (disciplines), Context (language use), Biology, Models, Biological, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, 03 medical and health sciences, symbols.namesake, Environmental rDNA sequencing, Sequence Homology, Nucleic Acid, medicine, Animals, Ciliophora, Ecosystem, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic diversity, [SDV.GEN]Life Sciences [q-bio]/Genetics, Base Sequence, Biochemistry, Genetics and Molecular Biology(all), Genetic Variation, Cell Biology, Multicellular organism, Biological dispersal, Animal Migration, human activities, Developmental Biology
Abstract: Background High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. Results Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals. Conclusions Currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0125-5) contains supplementary material, which is available to authorized users.
Published: 2015
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23. PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments

Author: Cedric Notredame, Vladimir Keduas, Frederic Reinier, Stéphane Audic, Olivier Poirot, Fabrice Armougom, and Sébastien Moretti
Subjects: Genetics, Internet, Sequence profiling tool, Multiple sequence alignment, Base Sequence, Sequence analysis, Structural alignment, Sequence alignment, DNA, Biology, Article, User-Computer Interface, Sequence logo, Genes, Sequence Analysis, Protein, RefSeq, Consensus sequence, RNA, Messenger, Sequence Alignment, Software
Abstract: We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify the gene sequence. This gene sequence is then aligned with the query protein using Exonerate in order to extract a coding nucleotide sequence matching the original protein. Protogene can handle protein fragments and will return every CDS coding for a given protein, even if they occur in different genomes. Protogene is available from http://www.tcoffee.org/.
Published: 2006
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24. Rickettsia felis, from Culture to Genome Sequencing

Author: Patricia Renesto, Stéphane Audic, Pierre-Edouard Fournier, Didier Raoult, Guillaume Blanc, Jean-Michel Claverie, Catherine Robert, Hiroyuki Ogata, and Sylvianne Robineau
Subjects: DNA, Bacterial, Genetics, Bacteriological Techniques, biology, Sequence analysis, General Neuroscience, Sequence Analysis, DNA, biology.organism_classification, Genome, Rickettsia felis, General Biochemistry, Genetics and Molecular Biology, Pilus, Microbiology, Plasmid maintenance, Plasmid, History and Philosophy of Science, Animals, Humans, Gene, Genome, Bacterial, Bacteria
Abstract: Rickettsia felis has been recently cultured in XTC2 cells. This allows production of enough bacteria to create a genomic bank and to sequence it. The chromosome of R. felis is longer than that of previously sequenced rickettsiae and it possess 2 plasmids. Microscopically, this bacterium exhibits two forms of pili: one resembles a conjugative pilus and another forms hair-like projections that may play a role in pathogenicity. R. felis also exhibits several copies of ankyrin-repeat genes and tetratricopeptide encoding gene that are specifically linked to pathogenic host-associated bacteria. It also contains toxin-antitoxin system encoding genes that are extremely rare in intracellular bacteria and may be linked to plasmid maintenance.
Published: 2005
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25. Some lessons fromRickettsiagenomics

Author: Hiroyuki Ogata, Stéphane Audic, Jean-Michel Claverie, Didier Raoult, and Patricia Renesto
Subjects: Comparative genomics, Genetics, biology, Molecular Sequence Data, Genomics, biology.organism_classification, Rickettsial Vaccines, Microbiology, Genome, Rickettsiaceae, Rickettsia prowazekii, Rickettsia conorii, Infectious Diseases, Rickettsia, Genes, Bacterial, Amino Acid Sequence, Genome, Bacterial
Abstract: Sequencing of the Rickettsia conorii genome and its comparison with its closest sequenced pathogenic relative, i.e., Rickettsia prowazekii, provided powerful insights into the evolution of these microbial pathogens. However, advances in our knowledge of rickettsial diseases are still hindered by the difficulty of working with strict intracellular bacteria and their hosts. Information gained from comparing the genomes of closely related organisms will shed new light on proteins susceptible to be targeted in specific diagnostic assays, by new antimicrobial drugs, and that could be employed in the generation of future rickettsial vaccines. In this review we present a detailed comparison of the metabolic pathways of these bacteria as well as the polymorphisms of their membrane proteins, transporters and putative virulence factors. Environmental adaptation of Rickettsia is also discussed.
Published: 2005
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26. The 1.2-Megabase Genome Sequence of Mimivirus

Author: Catherine Robert, Didier Raoult, Stéphane Audic, Jean-Michel Claverie, Chantal Abergel, Hiroyuki Ogata, Bernard La Scola, Marie Suzan, and Patricia Renesto
Subjects: Protein Folding, DNA Repair, Genes, Viral, Proteome, Molecular Sequence Data, Acanthamoeba, Genome, Viral, Nucleocytoplasmic large DNA viruses, Genome, Inteins, Open Reading Frames, Viral Proteins, RNA, Transfer, Animals, Megaviridae, Giant Virus, Phylogeny, Genetics, Base Composition, Mimivirus, Multidisciplinary, biology, Pandoravirus, DNA Viruses, Computational Biology, Sequence Analysis, DNA, biology.organism_classification, Introns, Enzymes, Protein Biosynthesis, DNA, Viral, RNA, Viral, Megavirus, Cafeteria roenbergensis virus, DNA Topoisomerases
Abstract: We recently reported the discovery and preliminary characterization of Mimivirus, the largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is a double-stranded DNA virus growing in amoebae. We now present its 1,181,404–base pair genome sequence, consisting of 1262 putative open reading frames, 10% of which exhibit a similarity to proteins of known functions. In addition to exceptional genome size, Mimivirus exhibits many features that distinguish it from other nucleocytoplasmic large DNA viruses. The most unexpected is the presence of numerous genes encoding central protein-translation components, including four amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. The size and complexity of the Mimivirus genome challenge the established frontier between viruses and parasitic cellular organisms. This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes.
Published: 2004
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27. Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

Author: Camille, Clerissi, Yves, Desdevises, Sarah, Romac, Stéphane, Audic, Colomban, de Vargas, Silvia G, Acinas, Raffaella, Casotti, Julie, Poulain, Patrick, Wincker, Pascal, Hingamp, Hiroyuki, Ogata, and Nigel, Grimsley
Subjects: Genotype, Chlorophyta, DNA, Viral, High-Throughput Nucleotide Sequencing, Phycodnaviridae, Biodiversity, Environment, Indian Ocean
Abstract: High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey-predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.
Published: 2015

28. PFR²: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution

Author: Raphaël, Morard, Kate F, Darling, Frédéric, Mahé, Stéphane, Audic, Yurika, Ujiié, Agnes K M, Weiner, Aurore, André, Heidi A, Seears, Christopher M, Wade, Frédéric, Quillévéré, Christophe J, Douady, Gilles, Escarguel, Thibault, de Garidel-Thoron, Michael, Siccha, Michal, Kucera, and Colomban, de Vargas
Subjects: Phylogeography, Rhizaria, Molecular Sequence Data, RNA, Ribosomal, 18S, Cluster Analysis, Biodiversity, Foraminifera, Sequence Analysis, DNA, DNA, Protozoan, Databases, Nucleic Acid, Plankton, DNA, Ribosomal, Ecosystem
Abstract: Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR(2), the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR(2) website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.
Published: 2015

29. Determinants of community structure in the global plankton interactome

Author: Colomban de Vargas, Stéphane Audic, Isabel Ferrera, Gabriel Gorsky, Jean Weissenbach, Guillem Salazar, Johan Decelle, Pablo Sánchez, Marta Royo-Llonch, Patrick Wincker, Francesco d'Ovidio, Jun Wang, Léo Berline, Ana María Cabello, Tara Oceans Coordinators, Marie-José Garet-Delmas, Simon Roux, Silvia G. Acinas, J. Cesar Ignacio-Espinosa, Peer Bork, Fabrice Not, Fabrizio Carcillo, Lars Stemmann, Hiroyuki Ogata, Marc Picheral, Chris Bowler, Céline Dimier, Nicolas Henry, Luc De Meester, Youssef Darzi, Eric Karsenti, Elena Lara, Shinichi Sunagawa, Francisco M. Cornejo-Castillo, Sébastien Colin, Stephane Pesant, Sabrina Speich, Karoline Faust, Marta Sebastián, Samuel Chaffron, Lionel Guidi, Caroline Souffreau, Jeroen Raes, Laurent Coppola, Sarah Searson, Stefanie Kandels-Lewis, Gipsi Lima-Mendez, Flora Vincent, Lucie Bittner, Gianluca Bontempi, Matthew B. Sullivan, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, 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), Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Processus de couplage à Petite Echelle, Ecosystèmes et Prédateurs Supérieurs (PEPS), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Biology and Oceanography [Barcelone], Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Pangea, Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Universidad de Granada = University of Granada (UGR), European Molecular Biology Laboratory [Heidelberg] (EMBL), Diversité et Interactions au sein du Plancton Océanique (DIPO), Institute for Chemical Research, Kyoto University, Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-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), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (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 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), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Department of Marine Biology and Oceanography, Universidad de Granada (UGR), Kyoto University [Kyoto], Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: Abiotic component, Biotic component, Multidisciplinary, Primary producers, Ecology, fungi, Community structure, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], 15. Life on land, Biology, Plankton, Interactome, Food chain, 13. Climate action, Abundance (ecology), 14. Life underwater, ComputingMilieux_MISCELLANEOUS
Abstract: Lima-Mendez, Gipsi ... et. al.-- 9 pages, 4 figures, 1 table, supplementary materials www.sciencemag.org/content/348/6237/1262073/suppl/DC1, Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated networkgenerated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models. © 2015, American Association for the Advancement of Science. All rights reserved, We thank the commitment of the following people and sponsors:Centre National de la Recherche Scientifique (CNRS) (in particular, Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Fund for Scientific Research – Flanders (G.L.M., K.F., S.C., and J.R.), Rega Institute (J.R.), KU Leuven(J.R.), The French Ministry of Research, the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), ANR (projects POSEIDON/ANR-09-BLAN-0348, PHYTBACK/ANR-2010-1709-01, PROMETHEUS/ANR-09-PCSGENM- 217, TARA GIRUS/ANR-09-PCS-GENM-218, European Union FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376, ERC Advanced Grant Awards to CB (Diatomite: 294823), Gordon and Betty Moore Foundation grant (3790) to M.B.S., Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to S.G.A., TANIT (CONES 2010-0036) from the Agència de Gestió d´Ajusts Universitaris i Reserca funded to S.G.A., JSPS KAKENHI grant number 26430184 to H.O., FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the EDF Foundation, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner, and its captain and crew. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that graciously granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015
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30. Eukaryotic plankton diversity in the sunlit ocean

Author: Jean-Marc Aury, Daniele Iudicone, Hiroyuki Ogata, Stéphane Audic, Frédéric Mahé, Fabrice Not, Johan Decelle, Gabriel Gorsky, Silvia G. Acinas, Pascal Hingamp, Sarah Romac, Noan Le Bescot, Matthieu Mulot, Sébastien Colin, Eleonora Scalco, Michael E. Sieracki, Marc Picheral, Tara Oceans Coordinators, Nicolas Henry, Stephane Pesant, Micah Dunthorn, Adriana Zingone, Sabrina Speich, Margaux Carmichael, Chris Bowler, Sarah Searson, Céline Dimier, Jeroen Raes, Gipsi Lima-Mendez, Shruti Malviya, Aleš Horák, Eric Karsenti, Ramiro Logares, Olga Flegontova, Julius Lukeš, Shinichi Sunagawa, Flora Vincent, Stefanie Kandels-Lewis, Enrique Lara, Raphael Morard, Stefan Engelen, Peer Bork, Patrick Wincker, Colomban de Vargas, Raffaele Siano, Ian Probert, Jean Weissenbach, Lars Stemmann, Cédric Berney, Samuel Chaffron, Olivier Jaillon, Lionel Guidi, Julie Poulain, Lucie Bittner, Nigel Grimsley, 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), 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, 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), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of ecology, Universität Kaiserslautern, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Immunobiologie Cellulaire et Moléculaire des Infections Parasitaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Oceanography, University of Hawai‘i [Mānoa] (UHM), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Faculty of Informatics [Brno] (FI / MUNI), Masaryk University [Brno] (MUNI), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Département Electronique, Optronique et Signal (DEOS), Institut Supérieur de l'Aéronautique et de l'Espace (ISAE-SUPAERO), Stazione Zoologica Anton Dohrn (SZN), European Molecular Biology Laboratory [Heidelberg] (EMBL), European Molecular Biology Laboratory [Grenoble] (EMBL), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory, Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Kaiserslautern (TU Kaiserslautern), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), CNRS [GDR3280], EMBL, Agency for Administration of University and Research Grants (AGAUR) [CONES 2010-0036], Veolia Environment Foundation, EBI [PRJEB402, PRJEB6610], Genoscope/CEA, Lorient Agglomeration, Illumina, UNIMIB, Electricite de France Foundation, Fondation pour la Recherche sur la Biodiversite, Tara schooner, Fund for Scientific Research - The French Ministry of Research, French Government [ANR-11-BTBR-0008, ANR-10-INBS-09-08, ANR-10-LABX-54], French Ministry of Foreign Affairs, UPMC, European Research Council [294823], VIB, Stazione Zoologica Anton Dohrn, Rega Institute, Japan Society for the Promotion of Science [26430184], KU Leuven, PSL* Research University [ANR-11-IDEX-0001-02], World Courier, ANR [POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, PHYTBACK/ANR-2010-1709-01, TARA-GIRUS/ANR-09-PCS-GENM-218], EU FP7 [287589, IHMS/HEALTH-F4-2010-261376], Gordon and Betty Moore Foundation [3790], Prince Albert II de Monaco Foundation, Spanish Ministry of Science and Innovation [CGL2011-26848/BOS], Diversité et Interactions au sein du Plancton Océanique ( DIPO ), Adaptation et diversité en milieu marin ( ADMM ), 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 ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Evolution des Protistes et Ecosystèmes Pélagiques ( EPEP ), Institut de biologie de l'ENS Paris (UMR 8197/1024) ( IBENS ), 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 ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie Paris-Seine, Institute of Molecular Biology and Swiss Institute of Bioinformatics, University of Zürich [Zürich] ( UZH ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR113-Institut National de la Santé et de la Recherche Médicale ( INSERM ), University of Hawaii at Manoa ( UHM ), Laboratoire d'océanographie de Villefranche ( LOV ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Faculty of Informatics [Masaryk], Masaryk University, Institut de Génomique, Genoscope, Centre National de Séquençage, MARUM, Universität Bremen Postfach, Dynamiques de l'Environnement Côtier ( DYNECO ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Département Electronique, Optronique et Signal ( DEOS ), Institut Supérieur de l'Aéronautique et de l'Espace ( ISAE-SUPAERO ), Stazione Zoologica Napoli, European Molecular Biology Laboratory [Heidelberg] ( EMBL ), European Molecular Biology Laboratory ( EMBL ), Biologie intégrative des organismes marins ( BIOM ), Observatoire océanologique de Banyuls ( OOB ), Information génomique et structurale ( IGS ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Kyoto University [Kyoto], Université Catholique de Louvain ( UCL ), Laboratoire de physique des océans ( LPO ), Institut de Recherche pour le Développement ( IRD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des Sciences de l'Environnement Marin (LEMAR) ( LEMAR ), Institut de Recherche pour le Développement ( IRD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Brest ( UBO ) -Institut Universitaire Européen de la Mer ( IUEM ), 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 ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Technische Universität Kaiserskautern, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] ( ICM ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (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 Paris), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Lausanne (UNIL), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), and Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Multidisciplinary, biology, [ SDV ] Life Sciences [q-bio], Ecology, Range (biology), [SDV]Life Sciences [q-bio], fungi, Rhizaria, Biodiversity, 15. Life on land, Ribosomal RNA, Plankton, biology.organism_classification, [ SDE ] Environmental Sciences, Phylogenetics, [SDE]Environmental Sciences, natural sciences, 14. Life underwater, Taxonomic rank, Ribosomal DNA
Abstract: Vargas, Colomban de ... et. al.-- 11 pages, 7 figures, supplementary materials www.sciencemag.org/content/348/6237/1261605/suppl/DC1, Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ∼150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ∼11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts. © 2015, American Association for the Advancement of Science. All rights reserved, We thank the following people and sponsors for their commitment: CNRS (in particular, the GDR3280); EMBL; Genoscope/CEA; UPMC; VIB; Stazione Zoologica Anton Dohrn; UNIMIB; Rega Institute; KU Leuven; Fund for Scientific Research – The French Ministry of Research, the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), and MEMO LIFE (ANR-10-LABX-54); PSL* Research University (ANR-11-IDEX-0001-02); ANR (projects POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCSGENM-217, PHYTBACK/ANR-2010-1709-01, and TARA-GIRUS/ANR-09-PCS-GENM-218); EU FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376); European Research Council Advanced Grant Awards to C. Bowler (Diatomite:294823); Gordon and Betty Moore Foundation grant 3790 to M.B.S.; Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS and TANIT (CONES 2010-0036) grant from the Agency for Administration of University and Research Grants (AGAUR) to S.G.A.; and Japan Society for the Promotion of Science KAKENHI grant 26430184 to H.O. We also thank the following for their support and commitment: A. Bourgois, E. Bourgois, R. Troublé, Région Bretagne, G. Ricono, the Veolia Environment Foundation, Lorient Agglomération, World Courier, Illumina, the Electricité de France Foundation, Fondation pour la Recherche sur la Biodiversité, the Prince Albert II de Monaco Foundation, and the Tara schooner and its captains and crew. We thank MERCATORCORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015
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31. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Author: Stéphane Audic, Colomban de Vargas, Désiré Tessier, Florence Le Gall, Ian Probert, El Mahdi Bendif, Sarah Romac, Adriana Lopes dos Santos, Michel D Guiry, Rowena Stern, Richard Christen, Daniel Vaulot, Adriana Zingone, Laure Guillou, Priscillia Gourvil, Johan Decelle, 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), Sir Alister Hardy Foundation for Ocean Science (SAHFOS), Marine Biological Association, Stazione Zoologica Anton Dohrn (SZN), The AlgaeBase Foundation, National University of Ireland [Galway] (NUI Galway), Diversité et Interactions au sein du Plancton Océanique (DIPO), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0106 biological sciences, plastidial 16S rRNA gene, diversity patterns, Molecular Sequence Data, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, DNA, Ribosomal, DNA sequencing, Molecular ecology, 03 medical and health sciences, Phylogenetics, life-cycle, RNA, Ribosomal, 16S, Genetics, picoeukaryote community structure, Cluster Analysis, phylogenetic analyses, Plastids, Gene, Ecology, Evolution, Behavior and Systematics, Phylogeny, atlantic-ocean, 030304 developmental biology, protists, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, cryptomonas cryptophyceae, photosynthesis, Ecology, 010604 marine biology & hydrobiology, high-throughput sequencing, Eukaryota, online resource, Genes, rRNA, DNA, Sequence Analysis, DNA, 15. Life on land, Amplicon, Taxon, marine picophytoplankton, 13. Climate action, Evolutionary biology, metabarcoding, phytoplankton, Taxonomy (biology), Databases, Nucleic Acid, Biotechnology
Abstract: International audience; Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
Published: 2014
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32. Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

Author: Noan, Le Bescot, Frédéric, Mahé, Stéphane, Audic, Céline, Dimier, Marie-José, Garet, Julie, Poulain, Patrick, Wincker, Colomban, de Vargas, and Raffaele, Siano
Subjects: Base Sequence, Ecology, Oceans and Seas, Phytoplankton, Dinoflagellida, RNA, Ribosomal, 18S, DNA Barcoding, Taxonomic, Biodiversity, DNA, Ribosomal
Abstract: Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V9 18S rDNA sequencing from 106 size-fractionated plankton communities collected across the world's surface oceans during the Tara Oceans expedition (2009-2012) to assess patterns of pelagic dinoflagellate diversity and community structuring over global taxonomic and ecological scales. Our data and analyses suggest that dinoflagellate diversity has been largely underestimated, representing overall ∼ 1/2 of protistan rDNA metabarcode richness assigned at ≥ 90% to a reference sequence in the world's surface oceans. Dinoflagellate metabarcode diversity and abundance display regular patterns across the global scale, with different order-level taxonomic compositions across organismal size fractions. While the pico to nano-planktonic communities are composed of an extreme diversity of metabarcodes assigned to Gymnodiniales or are simply undetermined, most micro-dinoflagellate metabarcodes relate to the well-referenced Gonyaulacales and Peridiniales orders, and a lower abundance and diversity of essentially symbiotic Peridiniales is unveiled in the meso-plankton. Our analyses could help future development of biogeochemical models of pelagic systems integrating the separation of dinoflagellates into functional groups according to plankton size classes.
Published: 2014

33. 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

34. Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

Author: Sarah Romac, Cédric Berney, Colomban de Vargas, Stéphane Audic, Finlay Maguire, Aurélie Chambouvet, Thomas A. Richards, Life Sciences London, The Natural History Museum [London] (NHM), 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), University of Exeter, and Marine Spatial Ecology Lab, School of BioSciences, University of Exeter
Subjects: Microbiology (medical), Geologic Sediments, Lineage (evolution), Molecular Sequence Data, Parvilucifera, medicine.disease_cause, Microbiology, DNA, Ribosomal, Perkinsus, Phylogenetics, medicine, RNA, Ribosomal, 18S, Animals, Cluster Analysis, Perkinsea, 14. Life underwater, Phylogeny, Phylotype, Phylogenetic tree, biology, Ecology, Protist, fungi, Genetic Variation, Food web, Sequence Analysis, DNA, DNA, Helminth, DNA, Protozoan, biology.organism_classification, Parasite, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolutionary biology, Alveolata, Pyrosequencing, 454 pyrosequencing, Research Article
Abstract: International audience; Background: Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity 'tag' sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations. Results: We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity suggesting this diversity encompasses a range of biologically and ecologically distinct organisms. Conclusions: These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally 'active' and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the 'seed bank' microbial community.
Published: 2014
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35. Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

Author: Michael E. Sieracki, Stéphane Audic, Ramon Massana, Ramiro Logares, Javier del Campo, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Instituto de Ciencia de Materiales de Aragón [Saragoza, España] (ICMA-CSIC), University of Zaragoza - Universidad de Zaragoza [Zaragoza], 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), project FLAME (MICINN, Spain) [CGL2010-16304], project BioMarKs (ERA-net Biodiversa, EU) [2008-6530], Marie Curie Fellowship [PIEF-GA-2009-235365], Juan de la Cierva program [JCI-2010-06594], and Spanish Network of Supercomputing [BCV-2010-3-0003, 2011-2-0003/3-0005]
Subjects: Oceans and Seas, [SDV]Life Sciences [q-bio], Biodiversity, MAST, pyrotags, Biology, Ecological transitions, Microbiology, Ribotyping, 03 medical and health sciences, Phylogenetics, Polyphyly, RNA, Ribosomal, 18S, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Genetic diversity, 18S rDNA, 030306 microbiology, Geomicrobiology, Ecology, fungi, MOCH, Genetic Variation, 15. Life on land, Plankton, Environmental biotechnology, Pyrotags, ecological transitions, SAG, [SDE]Environmental Sciences, Pyrosequencing, Original Article, Stramenopiles, Phylogenetic nomenclature
Abstract: 13 pages, 3 figures, 4 tables, Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists. A large part of this diversity belongs to basal heterotrophic stramenopiles and is distributed in a set of polyphyletic ribogroups (described from rDNA sequences) collectively named as MAST (MArine STramenopiles). In the few groups investigated, MAST cells are globally distributed and abundant bacterial grazers, therefore having a putatively large impact on marine ecosystem functioning. The main aim of this study is to reevaluate the MAST ribogroups described so far and to determine whether additional groups can be found. For this purpose, we used traditional and state-of-the-art molecular tools, combining 18S rDNA sequences from publicly available clone libraries, single amplified genomes (SAGs) of planktonic protists, and a pyrosequencing survey from coastal waters and sediments. Our analysis indicated a final set of 18 MAST groups plus 5 new ribogroups within Ochrophyta (named as MOCH). The MAST ribogroups were then analyzed in more detail. Seven were typical of anoxic systems and one of oxic sediments. The rest were clearly members of oxic marine picoplankton. We characterized the genetic diversity within each MAST group and defined subclades for the more diverse (46 subclades in 8 groups). The analyses of sequences within subclades revealed further ecological specializations. Our data provide a renovated framework for phylogenetic classification of the numerous MAST ribogroups and support the notion of a tight link between phylogeny and ecological distribution. These diverse and largely uncultured protists are widespread and ecologically relevant members of marine microbial assemblages, Financial support has been provided by projects FLAME (CGL2010-16304, MICINN, Spain) and BioMarKs (2008-6530, ERA-net Biodiversa, EU) to RM and by the Marie Curie Fellowship (PIEF-GA-2009-235365) and Juan de la Cierva program (JCI-2010-06594) to RL
Published: 2014
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36. Patterns of Rare and Abundant Marine Microbial Eukaryotes

Author: David Bass, Jan Pawlowski, Fabrice Not, Angélique Gobet, John R. Dolan, Sarah Romac, Christophe Boutte, Patrick Wincker, Wiebe H. C. F. Kooistra, Richard Christen, Raffaele Siano, Bente Edvardsen, Ramiro Logares, Colomban de Vargas, Thorsten Stoeck, Thomas A. Richards, Jean-Michel Claverie, Massimo C. Pernice, Nathalie Simon, Stéphane Audic, Frédéric Mahé, Kamran Shalchian-Tabrizi, Lucie Bittner, Adriana Zingone, Sébastien Santini, Micah Dunthorn, Hiroyuki Ogata, Ramon Massana, Johan Decelle, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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), Department of life sciences, The Natural History Museum [London] (NHM), Department of ecology, Universität Kaiserslautern, Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn (SZN), Diversité et Interactions au sein du Plancton Océanique (DIPO), Education academy of computational life sciences, Tokyo Institute of Technology [Tokyo] (TITECH), Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génomique métabolique (UMR 8030), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Biosciences, Geoffrey Pope Builing, University of Exeter, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Geneva [Switzerland], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Rare biosphere, Biogeography, Molecular Sequence Data, Rare species, Biodiversity, Marine Biology, microbial eukaryotes, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Species Specificity, abundance distribution, Abundance (ecology), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Mediterranean Sea, RNA, Ribosomal, 18S, Cluster Analysis, Ecosystem, 14. Life underwater, Picoplankton, Atlantic Ocean, Phylogeny, 030304 developmental biology, Population Density, 0303 health sciences, Agricultural and Biological Sciences(all), Base Sequence, Community, Biochemistry, Genetics and Molecular Biology(all), 030306 microbiology, Ecology, Microbiota, Eukaryota, High-Throughput Nucleotide Sequencing, marine, 15. Life on land, Europe, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, next-generation sequencing, North Sea, General Agricultural and Biological Sciences, community ecology
Abstract: Logares, Ramiro ... et. al.-- 9 pages, 5 figures, 1 table, Background. Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions. Results. Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change. Conclusions. We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time, We thank the Biodiversity of Marine euKaryotes (BioMarKs, http://www. biomarks.eu) consortium, which was funded by the European Union ERANet program BiodivERsA (2008-6530). Extra financial support was provided by the Marie Curie Intra-European Fellowship (PIEF-GA-2009-235365) and Juan de la Cierva (JCI-2010-06594) programmes to R.L. and FLAME (CGL2010-16304, MICINN, Spain) to R.M. The Barcelona Supercomputing Center (BSC) provided access to the MareNostrum supercomputer (grants BCV-2011-2-0003/3-0005 and 2012-1-0006/2-0002 to R.L. and R.M.)
Published: 2014
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37. Traitement d'impact fluide-solide par la méthode particulaire SPH

Author: Alain Combescure, Hariddh Bung, Marc Berthillier, and Stéphane Audic
Subjects: Turbine blade, Mechanical Engineering, Computation, Computational Mechanics, Structure (category theory), Geometry, Finite element method, Computational science, law.invention, Computational Mathematics, Mechanics of Materials, law, Modeling and Simulation, Code (cryptography), Mathematics
Abstract: A SPH method has been developed for the simulation of soft impacts of a fluid on a structure. The SPH method is coupled to a finite element method using a slave-master contact impact algorithm. An implementation has been performed in the Castem-Plexus explicit code. It is applied to bird swalling simulation in a turboreactor engine. The final strains and deformed shapes of the turbine blades are correctly predicted and the computation times are reasonable enough to do industrial applications.
Published: 2000
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38. Large-Scale Statistical Analyses of Rice ESTs Reveal Correlated Patterns of Gene Expression

Author: Stéphane Audic, Jean-Michel Claverie, Olivier Poirot, Rob M. Ewing, Alia Ben Kahla, and Fabrice Lopez
Subjects: Expressed Sequence Tags, Regulation of gene expression, Genetics, Expressed sequence tag, Letter, DNA, Complementary, Models, Statistical, Databases, Factual, Models, Genetic, biology, cDNA library, food and beverages, Oryza, Computational biology, biology.organism_classification, Contig Mapping, Gene Expression Regulation, Plant, Multigene Family, Gene expression, Arabidopsis thaliana, Cluster analysis, Gene, Functional genomics, Genetics (clinical)
Abstract: Large, publicly available collections of expressed sequence tags (ESTs) have been generated from Arabidopsis thaliana and rice (Oryza sativa). A potential, but relatively unexplored application of this data is in the study of plant gene expression. Other EST data, mainly from human and mouse, have been successfully used to point out genes exhibiting tissue- or disease-specific expression, as well as for identification of alternative transcripts. In this report, we go a step further in showing that computer analyses of plant EST data can be used to generate evidence of correlated expression patterns of genes across various tissues. Furthermore, tissue types and organs can be classified with respect to one another on the basis of their global gene expression patterns. As in previous studies, expression profiles are first estimated from EST counts. By clustering gene expression profiles or whole cDNA library profiles, we show that genes with similar functions, or cDNA libraries expected to share patterns of gene expression, are grouped together. Promising uses of this technique include functional genomics, in which evidence of correlated expression might complement (or substitute for) those of sequence similarity in the annotation of anonymous genes and identification of surrogate markers. The analysis presented here combines the application of a correlation-based clustering method with a graphical color map allowing intuitive visualization of patterns within a large table of expression measurements.
Published: 1999
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39. Self-identification of protein-coding regions in microbial genomes

Author: Stéphane Audic and Jean-Michel Claverie
Subjects: DNA, Bacterial, Genetics, Base Composition, Multidisciplinary, Bacteria, Models, Genetic, Phylogenetic tree, Markov chain, Reproducibility of Results, Bacterial genome size, Computational biology, Biological Sciences, Biology, Markov model, Genome, Partition (database), Markov Chains, genomic DNA, Bacterial Proteins, Genetic Techniques, Algorithms, Genome, Bacterial, Coding (social sciences)
Abstract: A new method for predicting protein-coding regions in microbial genomic DNA sequences is presented. It uses an ab initio iterative Markov modeling procedure to automatically perform the partition of genomic sequences into three subsets shown to correspond to coding, coding on the opposite strand, and noncoding segments. In contrast to current methods, such as genemark [Borodovsky, M. & McIninch, J. D. (1993) Comput. Chem. 17, 123–133], no training set or prior knowledge of the statistical properties of the studied genome are required. This new method tolerates error rates of 1–2% and can process unassembled sequences. It is thus ideal for the analysis of genome survey and/or fragmented sequence data from uncharacterized microorganisms. The method was validated on 10 complete bacterial genomes (from four major phylogenetic lineages). The results show that protein-coding regions can be identified with an accuracy of up to 90% with a totally automated and objective procedure.
Published: 1998
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40. Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context

Author: Sarah Romac, Frédéric Mahé, Colomban de Vargas, Thorsten Stoeck, Johannes Otto, Micah Dunthorn, Alexandros Stamatakis, Stéphane Audic, Simon Berger, Frank Kauff, Alexandra Stock, German Research Foundation, University of Kaiserslautern [Kaiserslautern], The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS ), Institute for Theoretical Informatics, Karlsruhe Institute of Technology (KIT), 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), Department of ecology, Universität Kaiserslautern, Deutsche Forschungsgemeinschaft (DFG) [DU1319/1-1], DFG [STA/860-3, STO414/3-1, STO414/3-2], European Funding Agencies from the ERAnet program BiodivERsA under the BioMarKs project [2008-6530], BioMarKS Consortium, and Carl-Zeiss post-doc grant
Subjects: 0106 biological sciences, SSU rDNA, Genetic Speciation, [SDV]Life Sciences [q-bio], Sequencing data, Genes, Protozoan, rDNA, Locus (genetics), Fresh Water, Biology, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, Marine-freshwater transitions, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, DNA, Ribosomal Spacer, Genetics, Colpodea, Seawater, Ciliophora, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, Models, Genetic, Ecology, Genetic Variation, High-Throughput Nucleotide Sequencing, SSU, Bayes Theorem, Sequence Analysis, DNA, Amplicon, biology.organism_classification, Ribosome Subunits, Small, Evolutionary biology, SSU-rDNA, [SDE]Environmental Sciences, Water Microbiology
Abstract: Dunthorn, Micah ... et al.-- 17 pages, 4 figures, 3 tables, 1 appendix, supplementary material http://mbe.oxfordjournals.org/content/31/4/993/suppl/DC1, Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments. © 2014 The Author, This work was supported by the Deutsche Forschungsgemeinschaft (DFG, grant DU1319/1-1) to M.D.; DFG (grant STA/860-3) to A.Sta.; European Funding Agencies from the ERAnet program BiodivERsA under the BioMarKs project (grant 2008-6530) to C.dV, T.S., and the BioMarKS Consortium; Carl-Zeiss postdoc grant to A.Sto.; and DFG (grants STO414/3-1 and STO414/3-2) to T.S.
Published: 2014
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41. The Significance of Digital Gene Expression Profiles

Author: Stéphane Audic and Jean-Michel Claverie
Subjects: DNA, Complementary, Gene Expression, Tumor cells, Computational biology, Biology, Bayes' theorem, Gene expression, Confidence Intervals, Tumor Cells, Cultured, Genetics, Humans, Dimethyl Sulfoxide, Serial analysis of gene expression, Pancreas, Gene, Genetics (clinical), Selection (genetic algorithm), Probability, Models, Statistical, Models, Genetic, cDNA library, Brain, Bayes Theorem, Actins, Differentially expressed genes, Liver, Sample Size, Tetradecanoylphorbol Acetate
Abstract: Genes differentially expressed in different tissues, during development, or during specific pathologies are of foremost interest to both basic and pharmaceutical research. “Transcript profiles” or “digital Northerns” are generated routinely by partially sequencing thousands of randomly selected clones from relevant cDNA libraries. Differentially expressed genes can then be detected from variations in the counts of their cognate sequence tags. Here we present the first systematic study on the influence of random fluctuations and sampling size on the reliability of this kind of data. We establish a rigorous significance test and demonstrate its use on publicly available transcript profiles. The theory links the threshold of selection of putatively regulated genes (e.g., the number of pharmaceutical leads) to the fraction of false positive clones one is willing to risk. Our results delineate more precisely and extend the limits within which digital Northern data can be used.
Published: 1997
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42. 454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

Author: Bente Edvardsen, Elianne Egge, Tom Andersen, Colomban de Vargas, Stéphane Audic, Lucie Bittner, Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), 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), Norwegian Research Council [190307 HAPTODIV], ASSEMBLE [227799], and EU
Subjects: 0106 biological sciences, DNA, Complementary, [SDV]Life Sciences [q-bio], lcsh:Medicine, 01 natural sciences, DNA, Ribosomal, DNA sequencing, Deep sequencing, Haptophyte, 03 medical and health sciences, lcsh:Science, Ribosomal DNA, Relative species abundance, Phylogeny, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, biology, 010604 marine biology & hydrobiology, lcsh:R, Species diversity, Haptophyta, High-Throughput Nucleotide Sequencing, Biodiversity, biology.organism_classification, Metagenomics, Evolutionary biology, [SDE]Environmental Sciences, Pyrosequencing, Metagenome, lcsh:Q, Research Article
Abstract: Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000–20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing. © 2013 Egge et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Published: 2013
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43. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author: Christophe Boutte, Raphael Morard, Gaëtan Burgaud, Micah Dunthorn, Pascal Zimmermann, David Bass, Noan Le Bescot, Laure Guillou, Fabrice Not, Bente Edvardsen, Enrique Lara, Dipankar Bachar, Colomban de Vargas, Thorsten Stoeck, Anne Laure Sauvadet, Marina Montresor, Jan Pawlowski, Cédric Berney, Daniel Vaulot, Maria Holzmann, Lucie Bittner, Ramon Massana, Johan Decelle, Javier del Campo, Wiebe H. C. F. Kooistra, Ramiro Logares, Richard Christen, Stéphane Audic, Frédéric Mahé, John R. Dolan, Raffaele Siano, Ian Probert, 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), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Department of life sciences, The Natural History Museum [London] (NHM), Groupe Plancton Océanique, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Instituto de Ciencia de Materiales de Aragón [Saragoza, España] (ICMA-CSIC), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Evolutionary Genetics, Stazione Zoologica Anton Dohrn (SZN), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Department of genetics and evolution, University of Geneva [Switzerland], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of ecology, Universität Kaiserslautern, Point Compétence Informatique, European Union [2008-6530, 287589], ANR (France), ANR Paralex (French), BIOMARKS, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], Computational biology, medicine.disease_cause, Ribosome, DNA, Ribosomal, DNA sequencing, 03 medical and health sciences, Genetics, medicine, DNA Barcoding, Taxonomic, Gene, 030304 developmental biology, Ribosome Subunits, Small, Eukaryotic, 0303 health sciences, Internet, biology, 030306 microbiology, fungi, Intron, Protist, Eukaryota, High-Throughput Nucleotide Sequencing, Genes, rRNA, Articles, Ribosomal RNA, biology.organism_classification, Molecular biology, RNA, Ribosomal, [SDE]Environmental Sciences, Eukaryote, Databases, Nucleic Acid, Cercozoa
Abstract: Laure Guillou ... et al. -- 8 pages, 1 figure, 1 table, The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists, The European Union’s Seventh Framework Programmes (FP7) BIOMARKS (2008-6530, ERA-net Biodiversa) and MicroB3 [287589] and the following ANR (France) projects: AQUAPARADOX, PARALEX and GIME. Funding for open access charge: ANR Paralex (French) and BIOMARKS (FP7)
Published: 2013
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44. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms

Author: Jan Pawlowski, Stéphane Audic, Sina Adl, David Bass, Lassaâd Belbahri, Cédric Berney, Samuel S Bowser, Ivan Cepicka, Johan Decelle, Micah Dunthorn, Anna Maria Fiore-Donno, Gillian H Gile, Maria Holzmann, Regine Jahn, Miloslav Jirků, Patrick J Keeling, Martin Kostka, Alexander Kudryavtsev, Enrique Lara, Julius Lukeš, David G Mann, Edward A D Mitchell, Frank Nitsche, Maria Romeralo, Gary W Saunders, Alastair G B Simpson, Alexey V Smirnov, John L Spouge, Rowena F Stern, Thorsten Stoeck, Jonas Zimmermann, David Schindel, Colomban de Vargas, Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), 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), University of Saskatchewan [Saskatoon] (U of S), Department of life sciences, The Natural History Museum [London] (NHM), Laboratory of Soil Biology, Université de Neuchâtel (UNINE), Wadsworth Center, Department of Zoology, University of Kaiserslautern [Kaiserslautern], Institute of Botany and Landscape Ecology, Universität Greifswald - University of Greifswald, Department of Biochemistry and Molecular Biology, Department of Evolutionary Genetics, Botanischer Garten und Botanischer Museum Berlin-Dahlem, Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Canadian Institute for Advanced Research (CIFAR), Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University (SPSPU)-Saint Petersburg State Polytechnical University (SPSPU), Laboratory of Soil Biodiversity, Royal Botanic Garden [Edinburgh], Universität zu Köln = University of Cologne, Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, University of New Brunswick (UNB), Department of Biology - Life Sciences Centre, Department of Invertebrate Zoology, National Center for Biotechnology Information (NCBI), Sir AlisterHardyFoundationforOceanScience, TheLaboratory,CitadelHill,PlymouthPL12PB,UK, Dept of Ecology, University of Kaiserslautern, Smithsonian Institution National Museum of Natural History (NMNH), Consortium for the Barcoding of Life, European ERA-net program BiodivErsA under the BioMarKs project, French ANR project [09-BLAN-0348 POSEIDON], Swiss National Science Foundation [31003A-140766], University of Geneva [Switzerland], Royal Botanical Garden Edinburgh, Royal Botanical Garden, and Universität zu Köln
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Biodiversity, Protozoology, medicine.disease_cause, 01 natural sciences, DNA barcoding, ddc:590, Community Page, Naturvetenskap, Biology (General), Phylogeny, 0303 health sciences, Ecology, General Neuroscience, Protist, Eukaryota, Plants, Eukaryotic Cells, [SDE]Environmental Sciences, Taxonomy (biology), Natural Sciences, General Agricultural and Biological Sciences, Genetic Markers, QH301-705.5, Biology, 010603 evolutionary biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, Microbial Ecology, 03 medical and health sciences, Species Specificity, Phylogenetics, medicine, RNA, Ribosomal, 18S, Genetics, Animals, DNA Barcoding, Taxonomic, Ecosystem, 030304 developmental biology, Internet, General Immunology and Microbiology, fungi, Genetic Variation, Genetic divergence, Multicellular organism, Species richness, Ribosomes, Zoology, Software
Abstract: Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth. Given their single-celled nature, discovering and describing new species has been difficult, and many protistan lineages contain a relatively small number of formally described species (Figure 1A), despite the critical importance of several groups as pathogens, environmental quality indicators, and markers of past environmental changes. It would seem natural to apply molecular techniques such as DNA barcoding to the taxonomy of protists to compensate for the lack of diagnostic morphological features, but this has been hampered by the extreme diversity within the group. The genetic divergence observed between and within major protistan groups greatly exceeds that found in each of the three multicellular kingdoms. No single set of molecular markers has been identified that will work in all lineages, but an international working group is now close to a solution. A universal DNA barcode for protists coupled with group-specific barcodes will enable an explosion of taxonomic research that will catalyze diverse applications.
Published: 2012
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45. Genome-Wide Analysis of Heteroduplex DNA in Mismatch Repair–Deficient Yeast Cells Reveals Novel Properties of Meiotic Recombination Pathways

Author: Emmanuelle Martini, Stéphane Audic, Valérie Borde, Bertrand Llorente, Bernard Dujon, Béatrice Regnault, Matthieu Legendre, Guillaume Soubigou, Institut de Radiobiologie Cellulaire et Moléculaire (IRCM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Dynamique nucléaire et plasticité du génome (DNPG), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), 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), Génopole, Institut Pasteur [Paris], Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM / U891 Inserm), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CNRS, Agence Nationale de la Recherche [ANR-10-BLAN-1606-03], Association pour la Recherche sur le Cancer (ARC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Institut Pasteur [Paris] (IP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and HAL-UPMC, Gestionnaire
Subjects: [SDE] Environmental Sciences, Cancer Research, DNA Repair, [SDV]Life Sciences [q-bio], Yeast and Fungal Models, DNA Mismatch Repair, Biochemistry, 0302 clinical medicine, Molecular cell biology, Chromosome Segregation, Holliday junction, DNA Breaks, Double-Stranded, Crossing Over, Genetic, Isomerases, Genetics (clinical), Genetics, Recombination, Genetic, 0303 health sciences, Enzyme Classes, Chromosome Biology, Nucleic Acid Heteroduplexes, Genomics, Branch migration, Cell biology, Enzymes, [SDV] Life Sciences [q-bio], Nucleic acids, Meiosis, MutS Homolog 2 Protein, [SDE]Environmental Sciences, DNA mismatch repair, Chromatid, Research Article, Saccharomyces cerevisiae Proteins, lcsh:QH426-470, DNA repair, DNA recombination, Saccharomyces cerevisiae, Mycology, Biology, Chromatids, Microbiology, Molecular Genetics, 03 medical and health sciences, Model Organisms, Sister chromatids, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, DNA, Cruciform, DNA synthesis, DNA structure, DNA, Yeast, lcsh:Genetics, MSH2, Homologous recombination, Sister Chromatid Exchange, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Meiotic DNA double-strand breaks (DSBs) initiate crossover (CO) recombination, which is necessary for accurate chromosome segregation, but DSBs may also repair as non-crossovers (NCOs). Multiple recombination pathways with specific intermediates are expected to lead to COs and NCOs. We revisited the mechanisms of meiotic DSB repair and the regulation of CO formation, by conducting a genome-wide analysis of strand-transfer intermediates associated with recombination events. We performed this analysis in a SK1 × S288C Saccharomyces cerevisiae hybrid lacking the mismatch repair (MMR) protein Msh2, to allow efficient detection of heteroduplex DNAs (hDNAs). First, we observed that the anti-recombinogenic activity of MMR is responsible for a 20% drop in CO number, suggesting that in MMR–proficient cells some DSBs are repaired using the sister chromatid as a template when polymorphisms are present. Second, we observed that a large fraction of NCOs were associated with trans–hDNA tracts constrained to a single chromatid. This unexpected finding is compatible with dissolution of double Holliday junctions (dHJs) during repair, and it suggests the existence of a novel control point for CO formation at the level of the dHJ intermediate, in addition to the previously described control point before the dHJ formation step. Finally, we observed that COs are associated with complex hDNA patterns, confirming that the canonical double-strand break repair model is not sufficient to explain the formation of most COs. We propose that multiple factors contribute to the complexity of recombination intermediates. These factors include repair of nicks and double-stranded gaps, template switches between non-sister and sister chromatids, and HJ branch migration. Finally, the good correlation between the strand transfer properties observed in the absence of and in the presence of Msh2 suggests that the intermediates detected in the absence of Msh2 reflect normal intermediates., Author Summary Sexual reproduction consists in fusing two complementary gametes carrying only one set of chromosomes (haploids) to form a cell with two sets of homologous chromosomes (diploid). Gametes are generated through meiosis, a specialized cell division occurring in diploid organisms. For proper meiotic division to occur, homologous chromosomes need physical connections acquired through recombination that exchange chromosome arms (crossovers) and thereby contribute to genetic diversity. Recombination is induced by numerous chromosome breakages, but only a subset yields crossover recombinants, the remaining yielding non-crossover recombinants. Control of crossover formation is poorly understood. For this reason, precise knowledge of the meiotic recombination mechanisms is essential. Current models are based on studies performed at a few loci in model organisms. We revisited these models using an original approach that allowed us to study the DNA scars left at all chromosome breakage sites during single meioses in baker's yeast. We found that crossover formation is more dynamic than anticipated, which led us to propose variations of current crossover formation models. We also revealed that a significant fraction of non-crossovers do not arise from the canonical pathway, raising the possibility of a common pathway with crossover formation.
Published: 2011
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46. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

Author: Axel Cloeckaert, Stéphane Audic, Michel S. Zygmunt, Magali Lescot, Jean-Michel Claverie, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), 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), and Infectiologie Animale et Santé Publique (UR IASP)
Subjects: Evolution, Biodiversité et Ecologie, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Zoology, Brucella pinnipedialis, BRUCELLA, BACTERIAL GENOME EVOLUTION, COMPARATIVE GENOMICS, Brucella, Genome, Biodiversity and Ecology, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, QH359-425, Bacterial Genome Evolution, Animals, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Whole genome sequencing, Comparative genomics, 0303 health sciences, Phylogenetic tree, biology, 030306 microbiology, Comparative Genomics, biology.organism_classification, bacterial infections and mycoses, Caniformia, Evolutionary biology, [SDE]Environmental Sciences, Cetacea, Genome, Bacterial, Brucella melitensis, Research Article
Abstract: Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups.
Published: 2011
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47. A Holistic Approach to Marine Eco-Systems Biology

Author: Poirot Olivier, Atsuko Tanaka, Johan Decelle, Sabrina Speich, Jeroen Raes, Aurelie Chambouvet, Peer Bork, Colomban De Vargas, Pascal Hingamp, Silvia De Monte, Chris Bowler, Silvia Acinas, Adriana Zingone, Jean-Michel Claverie, Eric Pelletier, LEILA TIRICHINE DELACOUR, Stéphane PESANT, Pascal Morin, Josep M Gasol, Corinne DA SILVA, Olivier Jaillon, Gwenael Piganeau, Nicole Poulton, Yves Desdevises, Emmanuel Boss, Raffaella Casotti, Carlos Pedrós-Alió, Eve Toulza, Gilles Reverdin, Alaguraj Veluchamy, Marina Montresor, Jean-Louis JAMET, Lucie Subirana, Hugo Sarmento, Ian Probert, Benjamin Noel, Jean-Marc AURY, Stéphane Audic, Julie Poulain, Gipsi Lima-Mendez, Daniele Iudicone, Francisco M. Cornejo-Castillo, Francesca Benzoni, Isabel Ferrera, Shinichi Sunagawa, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Karsenti, E, Acinas, S, Bork, P, Bowler, C, De Vargas, C, Raes, J, Sullivan, M, Arendt, D, Benzoni, F, Claverie, J, Follows, M, Gorsky, G, Hingamp, P, Iudicone, D, Jaillon, O, Kandels-Lewis, S, Krzic, U, Not, F, Ogata, H, Pesant, S, Reynaud, E, Sardet, C, Sieracki, M, Speich, S, Velayoudon, D, Weissenbach, J, Wincker, P, European Molecular Biology Laboratory [Heidelberg] (EMBL), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit [Brussels] (VUB), University of Arizona, Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Massachusetts Institute of Technology (MIT), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Stazione Zoologica di Napoli (SZN), Stazione Zoologica di Napoli, Génomique métabolique (UMR 8030), 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)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Universität Bremen, University College Dublin [Dublin] (UCD), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Bigelow Laboratory for Ocean Sciences, Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), DVIP Consulting, Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-09-BLAN-0348,POSEIDON,PrOtiSts EcologIcal bioDiversity in Tara-OceaNs(2009), ANR-08-BDVA-0003,BIOMARKS,Biodiversité des eucaryotes marins(2008), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), ANR-09-GENM-0032,TARA-GIRUS,Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans(2009), JAMET, Jean-Louis, Blanc - - POSEIDON2009 - ANR-09-BLAN-0348 - Blanc - VALID, Eranet sur la Biodiversité - Biodiversité des eucaryotes marins - - BIOMARKS2008 - ANR-08-BDVA-0003 - BDIV - VALID, Génomique et biotechnologies végétales - Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans. - - PROMETHEUS2009 - ANR-09-GENM-0031 - GENOM-BTV - VALID, Génomique et biotechnologies végétales - Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans - - TARA-GIRUS2009 - ANR-09-GENM-0032 - GENOM-BTV - VALID, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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), Vrije Universiteit Brussel (VUB), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Stazione Zoologica Anton Dohrn (SZN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR-09-BLAN-0348,POSEIDON(2009), Department of Bio-engineering Sciences, Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J., UCLouvain, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (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 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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano-Bicocca, Aix Marseille Université (AMU), Université de la Méditerranée - Aix-Marseille 2, Center for Marine Environmental Sciences [Bremen] (MARUM), Développement de l'enfant, Groupe de Biologie Marine du CEA, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), DVIPC, The Tara Oceans expedition is generously funded by CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR, FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation., and the Tara Oceans Consortium
Subjects: MESH: Oceans and Seas, Ecosystem modeling, Biodiversity, Marine and Aquatic Sciences, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Microbial ecology, Seas, Ecosystem model, Global Change Ecology, Community Page, Oceans, MESH: Plankton, [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, MESH: Animals, MESH: Ecosystem, Genome Sequencing, Biology (General), MESH: Expeditions, 0303 health sciences, Biological data, Ecology, General Neuroscience, Systems Biology, Environmental resource management, MESH: Marine Biology, Genomics, Biogeochemistry, Plankton, Community Ecology, Expeditions, General Agricultural and Biological Sciences, Marine ecosystems, BIO/05 - ZOOLOGIA, QH301-705.5, Systems biology, Oceans and Seas, Tara Oceans, Marine Biology, Biological Data Management, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, Carbon Cycle, Marine ecology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Systems Ecology, Animals, Marine ecosystem, 14. Life underwater, Biological oceanography, Ecosystem, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Marine biology, General Immunology and Microbiology, 030306 microbiology, business.industry, Computational Biology, xxx, 15. Life on land, Tara Oceans Consortium, Earth system science, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Geochemistry, 13. Climate action, Microbial Evolution, Earth Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Genome Expression Analysis, Environmental Sciences
Abstract: Eric Karsenti et al.-- 5 pages, 2 figures, With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosystems are crucial in the regulation of Earth's biogeochemical cycles and climate [6],[7]. Yet their organization, evolution, and dynamics remain poorly understood [8],[9]. The Tara Oceans project was launched in September 2009 for a 3-year study of the global ocean ecosystem aboard the ship Tara. A unique sampling programme encompassing optical and genomic methods to describe viruses, bacteria, archaea, protists, and metazoans in their physico-chemical environment has been implemented. Starting as a grassroots initiative of a few scientists, the project has grown into a global consortium of over 100 specialists from diverse disciplines, including oceanography, microbial ecology, genomics, molecular, cellular, and systems biology, taxonomy, bioinformatics, data management, and ecosystem modeling. This multidisciplinary community aims to generate systematic, open access datasets usable for probing the morphological and molecular makeup, diversity, evolution, ecology, and global impacts of plankton on the Earth system, We are keen to thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON, BIOMARKS, PROMETHEUS, and TARA-GIRUS), FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without the continuous support of the participating 23 institutes (see http://oceans.taraexpeditions.org). Special thanks also goes to Fabrice Not and Noan Le Bescot for creating the figures of this manuscript. This is contribution number 0001 of the Tara Oceans Expedition 2009–2012
Published: 2011
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48. BLAST-EXPLORER helps you building datasets for phylogenetic analysis

Author: Alexis Dereeper, Jean-Michel Claverie, Stéphane Audic, and Guillaume Blanc
Subjects: Phylogenetic tree, Evolution, Computational Biology, Sampling (statistics), ComputerApplications_COMPUTERSINOTHERSYSTEMS, Sequence Analysis, DNA, Biology, computer.software_genre, Homologous Sequences, Task (project management), User-Computer Interface, ComputingMethodologies_PATTERNRECOGNITION, Molecular evolution, Phylogenetics, Evolutionary biology, TheoryofComputation_LOGICSANDMEANINGSOFPROGRAMS, hemic and lymphatic diseases, Databases, Genetic, QH359-425, Data mining, computer, Software, Algorithms, Phylogeny, Ecology, Evolution, Behavior and Systematics
Abstract: Background The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. Results To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform. Conclusions BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr
Published: 2010

49. Brucella microti: the genome sequence of an emerging pathogen

Author: Stéphane Audic, Jean-Michel Claverie, Magali Lescot, and Holger C. Scholz
Subjects: DNA, Bacterial, Ochrobactrum anthropi, lcsh:QH426-470, lcsh:Biotechnology, Pseudogene, animal diseases, Molecular Sequence Data, Brucella, Biology, Genome, Ochrobactrum, lcsh:TP248.13-248.65, parasitic diseases, Genetics, Gene, Phylogeny, Whole genome sequencing, Comparative Genomic Hybridization, Base Sequence, Sequence Analysis, DNA, biology.organism_classification, bacterial infections and mycoses, lcsh:Genetics, RNA, Ribosomal, 23S, Phenotype, Genes, Bacterial, Brucella suis, Sequence Alignment, Genome, Bacterial, Pseudogenes, Biotechnology, Research Article
Abstract: Background Using a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella microti, was determined. B. microti is a member of the genus Brucella within the Alphaproteobacteria, which consists of medically important highly pathogenic facultative intracellular bacteria. In contrast to all other Brucella species, B. microti is a fast growing and biochemically very active microorganism with a phenotype more similar to that of Ochrobactrum, a facultative human pathogen. The atypical phenotype of B. microti prompted us to look for genomic differences compared to other Brucella species and to look for similarities with Ochrobactrum. Results The genome is composed of two circular chromosomes of 2,117,050 and 1,220,319 base pairs. Unexpectedly, we found that the genome sequence of B. microti is almost identical to that of Brucella suis 1330 with an overall sequence identity of 99.84% in aligned regions. The most significant structural difference between the two genomes is a bacteriophage-related 11,742 base pairs insert only present in B. microti. However, this insert is unlikely to have any phenotypical consequence. Only four protein coding genes are shared between B. microti and Ochrobactrum anthropi but impaired in other sequenced Brucella. The most noticeable difference between B. microti and other Brucella species was found in the sequence of the 23S ribosomal RNA gene. This unusual variation could have pleiotropic effects and explain the fast growth of B. microti. Conclusion Contrary to expectations from the phenotypic analysis, the genome sequence of B. microti is highly similar to that of known Brucella species, and is remotely related to the one of O. anthropi. How the few differences in gene content between B. microti and B. suis 1330 could result in vastly different phenotypes remains to be elucidated. This unexpected finding will complicate the task of identifying virulence determinants in the Brucella genus. The genome sequence of B. microti will serve as a model for differential expression analysis and complementation studies. Our results also raise some concerns about the importance given to phenotypical traits in the definition of bacterial species.
Published: 2009

50. The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'

Author: Stéphane Audic, Sabine Chenivesse, Audrey Lartigue, Renata Grzela, Chantal Abergel, Stéphanie Encinas, Deborah Byrne, and Jean-Michel Claverie
Subjects: DNA, Complementary, Letter, Polyadenylation, Molecular Sequence Data, Acanthamoeba, Genome, Viral, Biology, Genome, Evolution, Molecular, Open Reading Frames, RNA, Transfer, Genetics, Animals, RNA, Messenger, ORFS, Gene, Genetics (clinical), DNA Primers, Mimivirus, Palindrome, DNA Viruses, biology.organism_classification, Open reading frame, Transfer RNA
Abstract: Mimivirus, a giant DNA virus infecting Acanthamoeba, is revealing an increasing list of unique features such as a 1.2-Mb genome with numerous genes not found in other viruses, a uniquely conserved promoter signal, and a particle of unmatched complexity using two distinct portals for genome delivery and packaging. Herein, we contribute a further Mimivirus distinctive feature discovered by sequencing a panel of viral cDNAs produced for probing the structure of Mimivirus transcripts. All Mimivirus mRNAs are polyadenylated at a site coinciding exactly with unrelated, but strongly palindromic, genomic sequences. The analysis of 454 Life Sciences (Roche) FLX cDNA tags (150,651) confirmed this finding for all Mimivirus genes independent of their transcription timings and expression levels. The absence of a suitable palindromic signal between adjacent genes results in transcripts encompassing multiple ORFs in the same or even in opposite orientations. Surprisingly, Mimivirus tRNAs are expressed as polyadenylated messengers, including an ORF/tRNA composite mRNA. To our knowledge, both the nature and the stringency of the “hairpin rule” defining the location of polyadenylation sites are unique, raising once more the question of Mimivirus's evolutionary origin. The precise molecular mechanisms implementing the hairpin rule into the 3′-end processing of Mimivirus pre-mRNAs remain to be elucidated.
Published: 2009

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