%0 Journal Article %J Molecular Ecology Resources %D 2015 %T PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy %A Decelle, Johan %A Romac, Sarah %A Stern, Rowena F. %A Bendif, El Mahdi %A Zingone, Adriana %A Audic, Stéphane %A Guiry, Michael D. %A Guillou, Laure %A Tessier, Désiré %A Le Gall, Florence %A Gourvil, Priscillia %A dos Santos, Adriana Lopes %A Probert, Ian %A Vaulot, Daniel %A de Vargas, Colomban %A Christen, Richard %K 2015 %K MACUMBA %K rcc %K RCC?o?dd %K SBR$_\textrmP$hyto$_\textrmD$IPO %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %X 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. %B Molecular Ecology Resources %V 15 %P 1435–1445 %G eng %U http://doi.wiley.com/10.1111/1755-0998.12401 %R 10.1111/1755-0998.12401 %0 Journal Article %J PLoS biology %D 2014 %T The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing %A Keeling, Patrick J %A Burki, Fabien %A Wilcox, Heather M %A Allam, Bassem %A Allen, Eric E %A Amaral-Zettler, Linda A %A Armbrust, E Virginia %A Archibald, John M %A Bharti, Arvind K %A Bell, Callum J %A Beszteri, Bank %A Bidle, Kay D %A Cameron, Connor T %A Campbell, Lisa %A Caron, David A %A Cattolico, Rose Ann %A Collier, Jackie L %A Coyne, Kathryn %A Davy, Simon K %A Deschamps, Phillipe %A Dyhrman, Sonya T %A Edvardsen, Bente %A Gates, Ruth D %A Gobler, Christopher J %A Greenwood, Spencer J %A Guida, Stephanie M %A Jacobi, Jennifer L %A Jakobsen, Kjetill S %A James, Erick R %A Jenkins, Bethany %A John, Uwe %A Johnson, Matthew D %A Juhl, Andrew R %A Kamp, Anja %A Katz, Laura A %A Kiene, Ronald %A Kudryavtsev, Alexander %A Leander, Brian S %A Lin, Senjie %A Lovejoy, Connie %A Lynn, Denis %A Marchetti, Adrian %A McManus, George %A Nedelcu, Aurora M %A Menden-Deuer, Susanne %A Miceli, Cristina %A Mock, Thomas %A Montresor, Marina %A Moran, Mary Ann %A Murray, Shauna %A Nadathur, Govind %A Nagai, Satoshi %A Ngam, Peter B %A Palenik, Brian %A Pawlowski, Jan %A Petroni, Giulio %A Piganeau, Gwenael %A Posewitz, Matthew C %A Rengefors, Karin %A Romano, Giovanna %A Rumpho, Mary E %A Rynearson, Tatiana %A Schilling, Kelly B %A Schroeder, Declan C %A Simpson, Alastair G B %A Slamovits, Claudio H %A Smith, David R %A Smith, G Jason %A Smith, Sarah R %A Sosik, Heidi M %A Stief, Peter %A Theriot, Edward %A Twary, Scott N %A Umale, Pooja E %A Vaulot, Daniel %A Wawrik, Boris %A Wheeler, Glen L %A Wilson, William H %A Xu, Yan %A Zingone, Adriana %A Worden, Alexandra Z %K 2014 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %X Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans %B PLoS biology %V 12 %P e1001889 %G eng %U http://dx.doi.org/10.1371%252Fjournal.pbio.1001889 %R 10.1371/journal.pbio.1001889 %0 Journal Article %J Biogeochemistry %D 2007 %T A taxonomic review of the genus Phaeocystis %A Medlin, Linda %A Zingone, Adriana %K Molecular clock %K P. cordata %K P. globosa %K P. jahnii %K P. pouchetii %K P. scrobiculata %K Phaeocystis antarctica %K rcc3541 %K rDNA analysis %X Phaeocystis is recognized both as a nuisance and as an ecologicallyphytoplankton species. Its polymorphic life cycle with bothand flagellated cells causes many taxonomic problems. Sequenceamong 22 isolates representing a global distribution of thehas been compared using three molecular markers. The-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) spacer is tooto resolve species. The most conserved 18S ribosomalacid (rDNA) analysis suggests that an undescribedPhaeocystis sp. (isolate PLY559) is a sister taxon to theunicellular Phaeocystis jahnii; this clade branched priorthe divergence of all other Phaeocystis species, including theones. The internal transcribed spacer (ITS) region showsvariation that some spatial population structure can be, at least in P. antarctica. P. globosa and P. pouchetii havedifferent ITS copies, suggestive of cryptic species that areable to hybridize. A molecular clock has been constructed thatthe divergence of the cold water colonial forms from the-water colonial forms to be about 30 Ma and the divergence of P.and P. pouchetii to be about 15 Ma. A short description ofcolonial stage and the flagellated stage for each formallyspecies is provided. Morphological information is alsoon a number of undescribed species. These include the strain559, consisting of non-colonial cells with peculiar tubular, a second non-colonial species from the north westernSea producing a lot of mucus, and a colonial species with-less flagellates found in Italian waters. In addition, threemorphotypes with scales different from those of P.were reported in the literature from Antarctic waters. Theemerging from both molecular and morphological data is that theof species in the genus is still underestimated and that crypticpseudocryptic diversity requires a sound assessment in futureof this genus. Based on all published observations, an emendedof the genus is provided. %B Biogeochemistry %V 83 %P 3–18 %G eng %R 10.1007/s10533-007-9087-1