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<datestamp>2018-01-12</datestamp>
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<publisher>HAL CCSD</publisher>
<title lang=en>PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy</title>
<creator>Decelle, Johan</creator>
<creator>Romac, Sarah</creator>
<creator>Stern, Rowena F</creator>
<creator>Bendif, El Mahdi</creator>
<creator>Zingone, Adriana</creator>
<creator>Audic, Stéphane</creator>
<creator>Guiry, Michel D</creator>
<creator>Guillou, Laure</creator>
<creator>Tessier, Désiré</creator>
<creator>Le Gall, Florence</creator>
<creator>Gourvil, Priscillia</creator>
<creator>Lopes dos Santos, Adriana</creator>
<creator>Probert, Ian</creator>
<creator>Vaulot, Daniel</creator>
<creator>, </creator>
<creator>Christen, Richard</creator>
<contributor>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) - Université Pierre et Marie Curie - Paris 6 (UPMC) - Centre National de la Recherche Scientifique (CNRS)</contributor>
<contributor>Sir Alister Hardy Foundation for Ocean Science ; The Laboratory</contributor>
<contributor>Marine Biological Association ; Marine Biological Association</contributor>
<contributor>Stazione Zoologica Napoli</contributor>
<contributor>The AlgaeBase Foundation ; National University of Ireland [Galway] (NUI Galway)</contributor>
<contributor>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)</contributor>
<contributor>Evolution Paris Seine ; Université Nice Sophia Antipolis (UNS) ; Université Côte d'Azur (UCA) - Université Côte d'Azur (UCA) - Centre National de la Recherche Scientifique (CNRS) - Université des Antilles et de la Guyane (UAG) - Université Pierre et Marie Curie - Paris 6 (UPMC)</contributor>
<contributor>Adaptation et diversité en milieu marin (ADMM) ; Université Pierre et Marie Curie - Paris 6 (UPMC) - Centre National de la Recherche Scientifique (CNRS)</contributor>
<description>International audience</description>
<source>ISSN: 1755-098X</source>
<source>EISSN: 1755-0998</source>
<source>Molecular Ecology Resources</source>
<publisher>Wiley/Blackwell</publisher>
<identifier>hal-01149047</identifier>
<identifier>http://hal.upmc.fr/hal-01149047</identifier>
<identifier>http://hal.upmc.fr/hal-01149047/document</identifier>
<identifier>http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf</identifier>
<source>http://hal.upmc.fr/hal-01149047</source>
<source>Molecular Ecology Resources, Wiley/Blackwell, 2015, 15 (6), pp.1435-1445. 〈10.1111/1755-0998.12401〉</source>
<identifier>DOI : 10.1111/1755-0998.12401</identifier>
<relation>info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.12401</relation>
<language>en</language>
<subject lang=en>protists</subject>
<subject lang=en>photosynthesis</subject>
<subject lang=en>plastidial 16S rRNA gene</subject>
<subject lang=en>metabarcoding</subject>
<subject lang=en>phytoplankton</subject>
<subject lang=en>high-throughput sequencing</subject>
<subject>[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy</subject>
<subject>[SDV.GEN] Life Sciences [q-bio]/Genetics</subject>
<type>info:eu-repo/semantics/article</type>
<type>Journal articles</type>
<description lang=en>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.</description>
<date>2015</date>
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