@article {LopesdosSantos2016, title = {Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters}, journal = {The ISME Journal}, volume = {11}, number = {2}, year = {2017}, note = {tex.mendeley-tags: 2016,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, month = {feb}, pages = {512{\textendash}528}, keywords = {2016, MACUMBA, MicroB3, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, issn = {1751-7362}, doi = {10.1038/ismej.2016.120}, url = {http://www.nature.com/doifinder/10.1038/ismej.2016.120}, author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Tragin, Margot and No{\"e}l, Mary-H{\'e}l{\`e}ne and Decelle, Johan and Romac, Sarah and Vaulot, Daniel} } @article {Ichinomiya2016, title = {Diversity and oceanic distribution of Parmales (Bolidophyceae), a picoplankton group closely related to diatoms}, journal = {The ISME Journal}, volume = {in press}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, keywords = {2016, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.1038/ismej.2016.38}, author = {Ichinomiya, Mutsuo and Lopes dos Santos, A and Gourvil, Priscillia and Yoshikawa, Shinya and Kamiya, Mitsunobu and Ohki, Kaori and Audic, S and de Vargas, Colomban and Vaulot, Daniel and Kuwata, Akira} } @article {Vannier2016, title = {Survey of the green picoalga Bathycoccus genomes in the global ocean}, journal = {Scientific Reports}, volume = {6}, number = {1}, year = {2016}, note = {tex.mendeley-tags: 2016,RCC1105,RCC715,RCC716,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, month = {dec}, pages = {37900}, keywords = {2016, RCC1105, RCC715, RCC716, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, issn = {2045-2322}, doi = {10.1038/srep37900}, url = {http://www.nature.com/articles/srep37900}, author = {Vannier, Thomas and Leconte, Jade and Seeleuthner, Yoann and Mondy, Samuel and Pelletier, Eric and Aury, Jean-Marc and de Vargas, Colomban and Sieracki, Michael and Iudicone, Daniele and Vaulot, Daniel and Wincker, Patrick and Jaillon, Olivier} } @article {Decelle2015, title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy}, journal = {Molecular Ecology Resources}, volume = {15}, number = {6}, year = {2015}, note = {tex.mendeley-tags: 2015,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {1435{\textendash}1445}, abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing 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 data- base 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 classifica- tion 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.}, keywords = {2015, MACUMBA, rcc, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, issn = {1755098X}, doi = {10.1111/1755-0998.12401}, url = {http://doi.wiley.com/10.1111/1755-0998.12401}, author = {Decelle, Johan and Romac, Sarah and Stern, Rowena F. and Bendif, El Mahdi and Zingone, Adriana and Audic, St{\'e}phane and Guiry, Michael D. and Guillou, Laure and Tessier, D{\'e}sir{\'e} and Le Gall, Florence and Gourvil, Priscillia and dos Santos, Adriana Lopes and Probert, Ian and Vaulot, Daniel and de Vargas, Colomban and Christen, Richard} } @article {Chambouvet2014, title = {Diverse molecular signatures for ribosomally {\textquoteright}active{\textquoteright} Perkinsea in marine sediments}, journal = {BMC Microbiology}, volume = {14}, number = {1}, year = {2014}, note = {tex.mendeley-tags: 2014,rcc,sbr?hyto?ppo}, pages = {110}, abstract = {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. 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 {\textquoteright}tag{\textquoteright} 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 as to suggest 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 {\textquoteright}active{\textquoteright} 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 {\textquoteright}seed bank{\textquoteright} microbial community.}, keywords = {2014, Biomarks, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1186/1471-2180-14-110}, url = {http://www.biomedcentral.com/1471-2180/14/110}, author = {Chambouvet, Aurelie and Berney, Cedric and Romac, Sarah and Audic, St{\'e}phane and Maguire, Finlay and de Vargas, Colomban and Richards, Thomas} } @article {Bendif2014, title = {Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta)}, journal = {Journal of Phycology}, volume = {50}, year = {2014}, note = {tex.mendeley-tags: 2014,cc3549,rcc,rcc1210,rcc1213,rcc1220,rcc1227,rcc1229,rcc1242,rcc1252,rcc1253,rcc1258,rcc1259,rcc1260,rcc1271,rcc1281,rcc1288,rcc1292,rcc1297,rcc1300,rcc1303,rcc1305,rcc1316,rcc1562,rcc174,rcc1839,rcc3545,rrcc1247,sbr?hyto?ppo}, pages = {140{\textendash}148}, keywords = {2014, cc3549, rcc, rcc1210, RCC1213, rcc1220, rcc1227, rcc1229, RCC1242, rcc1252, RCC1253, rcc1258, RCC1259, rcc1260, rcc1271, RCC1281, rcc1288, RCC1292, rcc1297, RCC1300, RCC1303, RCC1305, RCC1316, RCC1562, rcc174, RCC1839, rcc3545, rrcc1247, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1111/jpy.12147}, author = {Bendif, El Mahdi and Probert, Ian and Carmichael, Margaux and Romac, Sarah and Hagino, Kyoko and de Vargas, Colomban} } @article {Abida2013, title = {Bioprospecting marine plankton}, journal = {Marine Drugs}, volume = {11}, number = {11}, year = {2013}, note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {4594{\textendash}4611}, keywords = {2013, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.3390/md11114594}, url = {http://www.mdpi.com/1660-3397/11/11/4594}, author = {Abida, Heni and Ruchaud, Sandrine and Rios, Laurent and Humeau, Anne and Probert, Ian and de Vargas, Colomban and Bach, St{\'e}phane and Bowler, Chris} } @article {Bendif2013, title = {On the description of Tisochrysis lutea gen . nov . sp . nov . and Isochrysis nuda sp. nov. in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta)}, journal = {Journal of Applied Phycology}, volume = {25}, year = {2013}, note = {tex.mendeley-tags: 2013,RCC1195,RCC1207,RCC1281,RCC1286,RCC1344,RCC1346,RCC1347,RCC1348,RCC1349,RCC1350,RCC1353,RCC2477,RCC3681,RCC3684,RCC3686,RCC3687,RCC3690,RCC3691,RCC3692,RCC3693,RCC3694,RCC3695,RCC3696,RCC3699,RCC3701,RCC3707,rcc,sbr?hyto?ppo}, pages = {1763{\textendash}1776}, keywords = {2013, dicrateria, imantonia, isochrysidaceae, isochrysis galbana, phylogeny, rcc, RCC1195, RCC1207, RCC1281, RCC1286, RCC1344, RCC1346, RCC1347, RCC1348, RCC1349, RCC1350, RCC1353, RCC2477, RCC3681, RCC3684, RCC3686, RCC3687, RCC3690, RCC3691, RCC3692, RCC3693, RCC3694, RCC3695, RCC3696, RCC3699, RCC3701, RCC3707, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, taxonomy, ultrastructure}, doi = {10.1007/s10811-013-0037-0}, author = {Bendif, El Mahdi and Probert, Ian and Schroeder, Declan C and de Vargas, Colomban} } @article {Guillou2013, title = {The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {D597{\textendash}D604}, keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.1093/nar/gks1160}, author = {Guillou, Laure and Bachar, Dipankar and Audic, St{\'e}phane and Bass, David and Berney, Cedric and Bittner, Lucie and Boutte, Christophe and Burgaud, Gaetan and de Vargas, Colomban and Decelle, Johan and del Campo, Javier and Dolan, John and Dunthorn, Micah and Bente, Edvardsen and Holzmann, Maria and Kooistra, Wiebe H C F and Lara, Enrique and Lebescot, Noan and Logares, Ramiro and Mah{\'e}, Fr{\'e}d{\'e}ric and Massana, Ramon and Montresor, Marina and Morard, Raphael and Not, Fabrice and Pawlowski, Jan and Probert, Ian and Sauvadet, Anne-Laure and Siano, Raffaele and Stoeck, Thorsten and Vaulot, Daniel and Zimmermann, Pascal and Christen, Richard} } @article {Frada2012, title = {In situ survey of life cycle phases of the coccolithophore Emiliania huxleyi (Haptophyta)}, journal = {Environmental Microbiology}, volume = {14}, number = {6}, year = {2012}, note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo}, pages = {1558{\textendash}1569}, abstract = {The cosmopolitan coccolithophore Emiliania huxleyi is characterized by a strongly differentiated haplodiplontic life cycle consisting of a diploid phase, generally bearing coccoliths (calcified) but that can be also non-calcified, and a non-calcified biflagellated haploid phase. Given most studies have focused on the bloom-producing calcified phase, there is little-to-no information about non-calcified cells in nature. Using field mesocoms as experimental platforms, we quantitatively surveyed calcified and non-calcified cells using the combined calcareous detection fluorescent in situ hybridization (COD-FISH) method and qualitatively screened for haploid specific transcripts using reverse transcription-PCR during E. huxleyi bloom successions. Diploid, calcified cells formed dense blooms that were followed by the massive proliferation of E. huxleyi viruses (EhVs), which caused bloom demise. Non-calcified cells were also detected throughout the experiment, accounting for a minor fraction of the population but becoming progressively more abundant during mid-late bloom periods concomitant with EhV burst. Non-calcified cell growth also paralleled a distinct window of haploid-specific transcripts and the appearance of autotrophic flagellates morphologically similar to haploid cells, both of which are suggestive of meiosis and sexual life cycling during natural blooms of this prominent marine phytoplankton species.}, keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1111/j.1462-2920.2012.02745.x}, url = {http://dx.doi.org/10.1111/j.1462-2920.2012.02745.x}, author = {Frada, Miguel J and Bidle, Kay D and Probert, Ian and de Vargas, Colomban} } @article {Decelle2012, title = {An original mode of symbiosis in open ocean plankton}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, note = {tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo}, pages = {18000{\textendash}18005}, keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1073/pnas.1212303109}, author = {Decelle, J and Probert, I and Bittner, L and Desdevises, Y and Colin, S and de Vargas, C and Gali, M and Simo, R and Not, F} } @article {Hagino2011, title = {New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes}, journal = {Journal of Phycology}, volume = {47}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo}, pages = {1164{\textendash}1176}, abstract = {Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea.}, keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1111/j.1529-8817.2011.01053.x}, author = {Hagino, K and Bendif, El Mahdi and Young, J and Kogame, K and Takano, Y and Probert, I and Horiguchi, T and de Vargas, C and Okada, H} } @article {Beaufort2011, title = {Sensitivity of coccolithophores to carbonate chemistry and ocean acidification}, journal = {Nature}, volume = {476}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo}, pages = {80{\textendash}83}, abstract = {Coccolithophores produce the major fraction of pelagic carbonate, a key component of the carbon cycle. The effect of elevated CO2 on their calcification is poorly understood. Culture experiments have yielded varied calcification responses to increased pCO2 between and within coccolithophore taxa. We used a novel automated method for pattern recognition and morphometric analysis to quantify the calcite mass of coccolithophores from {\textquestiondown}700 samples from present past (last 40-Kyr) oceans. Comparison of morphological data with ocean carbonate chemistry reconstructed in both space and time indicate decreasing calcification with increasing pCO2, and decreasing CO32. At pH {\textexclamdown}8.0, delicate Emiliania huxleyi are strongly affected by decalcification. However, highly calcified E. huxleyi morphotypes predominate in waters with lowest pH. This suggests that coccolithophore strains pre-adapted to future, more acidic oceans already populate regions of contemporary oceans. The future carbon feedback from coccolithophore calcification will depend on the genetic diversity and adaptability of coccolithophore populations.}, keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1038/nature10295}, author = {Beaufort, L and Probert, I and de Garidel-Thoron, T and Bendif, E M and Ruiz-Pino, D and Metzl, N and Goyet, C and Buchet, N and Coupel, P and Grelaud, M and Rost, B and Rickaby, R E M and de Vargas, C} } @article {Rokitta2011, title = {Transcriptome analyses reveal differential gene expression patterns between the life-cycle stages of Emiliania huxleyi (Haptophyta) and reflect specialization to different ecological niches}, journal = {Journal of Phycology}, volume = {47}, number = {4}, year = {2011}, note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo}, pages = {829{\textendash}838}, abstract = {Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life-cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life-cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life-cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life-cycle stages are capable of particle uptake (0.5 ??m diameter) in late-stationary growth phase. Results showed that the two life-cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit.}, keywords = {2011, endocytosis, Life-cycle stages, microarray, quantitative RT-PCR, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, transcriptome profiling}, doi = {10.1111/j.1529-8817.2011.01014.x}, url = {http://dx.doi.org/10.1111/j.1529-8817.2011.01014.x}, author = {Rokitta, Sebastian D and de Nooijer, Lennart J and Trimborn, Scarlett and de Vargas, Colomban and Rost, Bj{\"o}rn and John, Uwe} } @article {Lepere2011, title = {Whole Genome Amplification (WGA) of marine photosynthetic eukaryote populations}, journal = {FEMS Microbiology Ecology}, volume = {76}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {516{\textendash}523}, keywords = {2011, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.1111/j.1574-6941.2011.01072.x}, author = {Lepere, Cecile and Demura, M and Kawachi, M and Romac, S and Probert, I and Vaulot, D} } @article {Frada2010, title = {A guide to extant coccolithophores (Calcihaptophycidae, Haptophyta) using light microscopy.}, journal = {Journal of Nannoplankton Research}, volume = {31}, year = {2010}, note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo}, pages = {58{\textendash}112}, keywords = {2010, ? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, author = {Frada, Miguel and Young, Jeremy and Cach{\~a}o, M{\'a}rio and Lino, S{\'\i}lvia and Martins, Ana and Narciso, {\'A}urea and Probert, Ian and de Vargas, Colomban} } @article {Siano2010, title = {Pelagodinium gen. nov. and P. beii comb. nov., a dinoflagellate symbiont of planktonic foraminifera}, journal = {Protist}, volume = {161}, year = {2010}, note = {tex.mendeley-tags: 2010,rcc,rcc1491,sbr?hyto?ppo}, pages = {385{\textendash}399}, abstract = {The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium b{\'e}ii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium b{\'e}ii is reclassified as Pelagodinium b{\'e}ii.}, keywords = {2010, ASSEMBLE, rcc, rcc1491, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1016/j.protis.2010.01.002}, author = {Siano, R and Montresor, M and Probert, I and Not, F and de Vargas, C} } @article {Liu2010, title = {A timeline of the environmental genetics of the haptophytes}, journal = {Molecular Biology and Evolution}, volume = {27}, year = {2010}, note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo}, pages = {171{\textendash}176}, abstract = {The use of genomic data and the rise of phylogenomics have radically changed our view of the eukaryotic tree of life at a high taxonomic level by identifying four to six "supergroups". Yet our understanding of the evolution of key innovations within each of these supergroups is limited because of poor species sampling relative to the massive diversity encompassed by each supergroup. Here we apply a multigene approach that incorporates a wide taxonomic diversity to infer the timeline of the emergence of strategic evolutionary transitions in the haptophytes, a group of ecologically and biogeochemically significant marine protists that belong to the Chromalveolata supergroup. Four genes (SSU, LSU, tufA and rbcL) were extensively analyzed under several Bayesian models to assess the robustness of the phylogeny, particularly with respect to (i) data partitioning, (ii) the origin of the genes (host vs. endosymbiont), (iii) across-site rate variation and (iv) across-lineage rate variation. We show with a relaxed clock analysis that the origin of haptophytes dates back to 824 MYA (95\% highest probability density 1031-637 MYA). Our dating results show that the ability to calcify evolved earlier than previously thought, between 329-291 MYA, in the Carboniferous period, and that the transition from mixotrophy to autotrophy occurred during the same time period. Although these two transitions precede a habitat change of major diversities from coastal / neritic waters to the pelagic realm (291-243 MYA, around the P/Tr boundary event), the emergence of calcification, full autotrophy and oceanic lifestyle seem mutually independent.}, keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1093/molbev/msp222}, url = {http://mbe.oxfordjournals.org/cgi/content/abstract/msp222v1}, author = {Liu, Hui and Aris-Brosou, Stephane and Probert, Ian and de Vargas, Colomban} } @article {Liu2009, title = {Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo}, pages = {12803{\textendash}12808}, keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1073/pnas.0905841106}, author = {Liu, H and Probert, I and Uitz, J and Claustre, H and Aris-Brossou, S and Frada, M and Not, F and de Vargas, C} } @article {Monier2009, title = {Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus}, journal = {Genome Research}, volume = {19}, year = {2009}, note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo}, pages = {1441{\textendash}1449}, keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1101/gr.091686.109}, author = {Monier, A and Pagarete, A and Allen, M J and Read, B A and de Vargas, C and Claverie, J M and Ogata, H} } @article {Richier2009, title = {Light-dependent transcriptional regulation of genes of biogeochemical interest in the diploid and haploid life cycle stages of Emiliania huxleyi}, journal = {Applied and Environmental Microbiology}, volume = {75}, year = {2009}, note = {Edition: 2009/03/24 ISBN: 1098-5336 (Electronic) tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo}, pages = {3366{\textendash}3369}, abstract = {The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested.}, keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1128/aem.02737-08}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=19304825}, author = {Richier, S and Kerros, M E and de Vargas, C and Haramaty, L and Falkowski, P G and Gattuso, J P} } @article {VonDassow2009, title = {Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell}, journal = {Genome Biology}, volume = {10}, number = {10}, year = {2009}, note = {tex.mendeley-tags: 2009,rcc,rcc1216,rcc1217,sbr?hyto?ppo}, pages = {R114}, abstract = {BACKGROUND:Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38000 Expressed Sequence Tags (ESTs) from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism.RESULTS:The haploid and diploid transcriptomes showed a dramatic differentiation, with [almost equal to]20\% greater transcriptome richness in diploid cells than in haploid cells and only [less than or equal to]50\% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog.CONCLUSIONS:This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined.}, keywords = {2009, rcc, RCC1216, rcc1217, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1186/gb-2009-10-10-r114}, url = {http://genomebiology.com/2009/10/10/R114}, author = {von Dassow, Peter and Ogata, Hiroyuki and Probert, Ian and Wincker, Patrick and Da Silva, Corinne and Audic, St{\'e}phane and Claverie, Jean-Michel and de Vargas, Colomban} } @article {Frada2008, title = {The {\textquotedblleft}Cheshire Cat{\textquotedblright} escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, note = {tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo}, pages = {15944{\textendash}15949}, abstract = {The coccolithophore is one of the most successful eukaryotes in modern oceans. The two phases in its haplodiploid life cycle exhibit radically different phenotypes. The diploid calcified phase forms extensive blooms, which profoundly impact global biogeochemical equilibria. By contrast, the ecological role of the noncalcified haploid phase has been completely overlooked. Giant phycodnaviruses ( viruses, EhVs) have been shown to infect and lyse diploid-phase cells and to be heavily implicated in the regulation of populations and the termination of blooms. Here, we demonstrate that the haploid phase of is unrecognizable and therefore resistant to EhVs that kill the diploid phase. We further show that exposure of diploid to EhVs induces transition to the haploid phase. Thus we have clearly demonstrated a drastic difference in viral susceptibility between life cycle stages with different ploidy levels in a unicellular eukaryote. Resistance of the haploid phase of provides an escape mechanism that involves separation of meiosis from sexual fusion in time, thus ensuring that genes of dominant diploid clones are passed on to the next generation in a virus-free environment. These {\^a}{\texteuro}{\oe}Cheshire Cat{\^a}{\texteuro} ecological dynamics release host evolution from pathogen pressure and thus can be seen as an opposite force to a classic {\^a}{\texteuro}{\oe}Red Queen{\^a}{\texteuro} coevolutionary arms race. In , this phenomenon can account for the fact that the selective balance is tilted toward the boom-and-bust scenario of optimization of both growth rates of calcifying cells and infectivity of EhVs.}, keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1073/pnas.0807707105}, author = {Frada, Miguel and Probert, Ian and Allen, Michael J and Wilson, William H and de Vargas, Colomban} } @article {Bowler2008, title = {The Phaeodactylum genome reveals the evolutionary history of diatom genomes}, journal = {Nature}, volume = {456}, number = {7219}, year = {2008}, note = {Publisher: Macmillan Publishers Limited. All rights reserved tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo}, pages = {239{\textendash}244}, keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPOdipo, sbr?hyto?ppo}, doi = {10.1038/nature07410}, url = {http://dx.doi.org/10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/suppinfo/nature07410_S1.html}, author = {Bowler, Chris and Allen, Andrew E and Badger, Jonathan H and Grimwood, Jane and Jabbari, Kamel and Kuo, Alan and Maheswari, Uma and Martens, Cindy and Maumus, Florian and Otillar, Robert P and Rayko, Edda and Salamov, Asaf and Vandepoele, Klaas and Beszteri, Bank and Gruber, Ansgar and Heijde, Marc and Katinka, Michael and Mock, Thomas and Valentin, Klaus and Verret, Frederic and Berges, John A and Brownlee, Colin and Cadoret, Jean-Paul and Chiovitti, Anthony and Choi, Chang Jae and Coesel, Sacha and De Martino, Alessandra and Detter, J Chris and Durkin, Colleen and Falciatore, Angela and Fournet, Jerome and Haruta, Miyoshi and Huysman, Marie J J and Jenkins, Bethany D and Jiroutova, Katerina and Jorgensen, Richard E and Joubert, Yolaine and Kaplan, Aaron and Kroger, Nils and Kroth, Peter G and La Roche, Julie and Lindquist, Erica and Lommer, Markus and Martin-Jezequel, Veronique and Lopez, Pascal J and Lucas, Susan and Mangogna, Manuela and McGinnis, Karen and Medlin, Linda K and Montsant, Anton and Secq, Marie-Pierre Oudot-Le and Napoli, Carolyn and Obornik, Miroslav and Parker, Micaela Schnitzler and Petit, Jean-Louis and Porcel, Betina M and Poulsen, Nicole and Robison, Matthew and Rychlewski, Leszek and Rynearson, Tatiana A and Schmutz, Jeremy and Shapiro, Harris and Siaut, Magali and Stanley, Michele and Sussman, Michael R and Taylor, Alison R and Vardi, Assaf and von Dassow, Peter and Vyverman, Wim and Willis, Anusuya and Wyrwicz, Lucjan S and Rokhsar, Daniel S and Weissenbach, Jean and Armbrust, E Virginia and Green, Beverley R and Van de Peer, Yves and Grigoriev, Igor V} }