PFR²: a curated database of planktonic Foraminifera18S ribosomal DNA as a resource for studies of plankton ecology, biogeography, and evolution

• Published in: Molecular Ecology Resources
• Main Authors: Morard, Raphaël, Darling, Kate F, Mahé, Frédéric, Audic, Stéphane, Ujiié, Yurika, Weiner, Agnes K.F., André, Aurore, Seears, Heidi, Wade, Chris M, Quillévéré, Frédéric, Douady, Christophe Jean, Escarguel, Gilles, de Garidel-Thoron, Thibault, Siccha, Michael, Kucera, Michal
• Other Authors: Center for Marine Environmental Sciences Bremen (MARUM), Universität Bremen, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff Roscoff (SBR), 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)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff Roscoff (SBR), 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)-Centre National de la Recherche Scientifique (CNRS), School of Geography and Geosciences St Andrews, University of St Andrews Scotland, School of Geosciences Edinburgh, University of Edinburgh (Edin.), Department of ecology, Technische Universität Kaiserslautern (TU Kaiserslautern), Department of biology, Shinshu University Nagano, URCA - UFR Sciences exactes et naturelles (URCA UFR SEN), Université de Reims Champagne-Ardenne (URCA), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences Bethlehem, Lehigh University, School of life sciences, University of Nottingham, UK (UON), Institut universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre Européen de Recherche et d'Enseignement des Géosciences de l'Environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2015
• Subjects: molecular ecology; 18S ribosomal DNA; planktonic foraminifera; genetic diversity; molecular taxonomy; sequence database; [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics; Phylogenetics and taxonomy; [SDV.GEN]Life Sciences [q-bio]/Genetics; [SDE]Environmental Sciences; Planktonic foraminifera
• Online Access: https://hal.sorbonne-universite.fr/hal-01149023; https://hal.sorbonne-universite.fr/hal-01149023v2/document; https://hal.sorbonne-universite.fr/hal-01149023v2/file/2015_morard.pdf; https://doi.org/10.1111/1755-0998.12410

International audience 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 PFR2, 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 PFR2 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.