title: PFR²: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.
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 We combined all available published and unpublished genetic data to build PFR(2), the Planktonic foraminifera Ribosomal Reference database.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.
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680, Roscoff, France.|Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680, Roscoff, France.|MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Morard
authors.affiliation: School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3JW, UK.|School of Geography and GeoSciences, University of St Andrews, Fife, KY16 9AL, UK.
authors.forename: Kate F
authors.initials: KF
authors.lastname: Darling
authors.affiliation: Department of Ecology, Technische Universität Kaiserslautern, 67663, Kaiserslautern, Germany.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Mahé
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680, Roscoff, France.|Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680, Roscoff, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Audic
authors.affiliation: Department of Biology, Shinshu University, Asahi3-1-1, Matsumoto, Nagano, 390-8621, Japan.
authors.forename: Yurika
authors.initials: Y
authors.lastname: Ujiié
authors.affiliation: MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany.
authors.forename: Agnes K M
authors.initials: AK
authors.lastname: Weiner
authors.affiliation: CNRS UMR 5276, Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Claude Bernard Lyon 1, 69622, Villeurbanne, France.|UFR Sciences Exactes et Naturelles, Université de Reims-Champagne-Ardenne, Campus Moulin de la Housse, Batiment 18, 51100, Reims, France.
authors.forename: Aurore
authors.initials: A
authors.lastname: André
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.|Department of Biological Sciences, Lehigh University, Iacocca Hall, 111 Research Drive, Bethlehem, PA, 18105, USA.
authors.forename: Heidi A
authors.initials: HA
authors.lastname: Seears
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Wade
authors.affiliation: CNRS UMR 5276, Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Claude Bernard Lyon 1, 69622, Villeurbanne, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Quillévéré
authors.affiliation: UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, ENTPE, CNRS, Université de Lyon, 6 rue Raphaël Dubois, 69622, Villeurbanne, France.|Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005, Paris, France.
authors.forename: Christophe J
authors.initials: CJ
authors.lastname: Douady
authors.affiliation: CNRS UMR 5276, Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Claude Bernard Lyon 1, 69622, Villeurbanne, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Escarguel
authors.affiliation: Aix-Marseille Université, CNRS, CEREGE UM34, Technopôle de l'Arbois, 13545, Aix-en-Provence, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: de Garidel-Thoron
authors.affiliation: MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Siccha
authors.affiliation: MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany.
authors.forename: Michal
authors.initials: M
authors.lastname: Kucera
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680, Roscoff, France.|Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680, Roscoff, France.
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
mesh_terms: D044822:Biodiversity; D016000:Cluster Analysis; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D030561:Databases, Nucleic Acid; D017753:Ecosystem; D056908:Foraminifera / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D058974:Phylogeography; D010933:Plankton / Q000145:classification / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D056901:Rhizaria; D017422:Sequence Analysis, DNA
chemical_list: D016054:DNA, Protozoan; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S
keywords: 18S ribosomal DNA; genetic diversity; molecular ecology; molecular taxonomy; planktonic foraminifera; sequence database