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dc.contributor.authorDecelle, Johan
dc.contributor.authorRomac, Sarah
dc.contributor.authorStern, Rowena F.
dc.contributor.authorBendif, El Mahdi
dc.contributor.authorZingone, Adriana
dc.contributor.authorAudic, Stéphane
dc.contributor.authorGuiry, Michael D.
dc.contributor.authorGuillou, Laure
dc.contributor.authorTessier, Désiré
dc.contributor.authorLe Gall, Florence
dc.contributor.authorGourvil, Priscillia
dc.contributor.authorDos Santos, Adriana L.
dc.contributor.authorProbert, Ian
dc.contributor.authorVaulot, Daniel
dc.contributor.authorde Vargas, Colomban
dc.contributor.authorChristen, Richard
dc.date.accessioned2018-09-20T16:05:31Z
dc.date.available2018-09-20T16:05:31Z
dc.date.issued2015-04-06
dc.identifier.citationDecelle, Johan; Romac, Sarah; Stern, Rowena F. Bendif, El Mahdi; Zingone, Adriana; Audic, Stéphane; Guiry, Michael D.; Guillou, Laure; Tessier, Désiré; Le Gall, Florence; Gourvil, Priscillia; Dos Santos, Adriana L.; Probert, Ian; Vaulot, Daniel; de Vargas, Colomban; Christen, Richard (2015). Phytoref: a reference database of the plastidial 16s rrna gene of photosynthetic eukaryotes with curated taxonomy. Molecular Ecology Resources 15 (6), 1435-1445
dc.identifier.issn1755-098X
dc.identifier.urihttp://hdl.handle.net/10379/11114
dc.description.abstractPhotosynthetic 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 (), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
dc.publisherWiley-Blackwell
dc.relation.ispartofMolecular Ecology Resources
dc.subjecthigh-throughput sequencing
dc.subjectmetabarcoding
dc.subjectphotosynthesis
dc.subjectphytoplankton
dc.subjectplastidial 16s rrna gene
dc.subjectprotists
dc.subjectpicoeukaryote community structure
dc.subjectcryptomonas cryptophyceae
dc.subjectmarine picophytoplankton
dc.subjectphylogenetic analyses
dc.subjectdiversity patterns
dc.subjectonline resource
dc.subjectatlantic-ocean
dc.subjectlife-cycle
dc.subjectphytoplankton
dc.subjectDNA
dc.titlePhytoref: a reference database of the plastidial 16s rrna gene of photosynthetic eukaryotes with curated taxonomy
dc.typeArticle
dc.identifier.doi10.1111/1755-0998.12401
dc.local.publishedsourcehttps://hal.sorbonne-universite.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
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