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      The Protist Ribosomal Reference database (PR 2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

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      1 , 2 , * , 3 , 4 , 1 , 2 , 5 ,   5 , 1 , 2 , 1 , 2 , 6 , 1 , 2 , 1 , 2 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 1 , 2 , 7 , 1 , 2 ,   7 , 12 , 1 , 2 , 1 , 2 , 11 , 14 , 15 , 1 , 2 , 16 , 9 , 1 , 2 , 17 , 3 , 4 , *
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR 2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.

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          Author and article information

          Journal
          Nucleic Acids Res
          Nucleic Acids Res
          nar
          nar
          Nucleic Acids Research
          Oxford University Press
          0305-1048
          1362-4962
          January 2013
          26 November 2012
          26 November 2012
          : 41
          : Database issue , Database issue
          : D597-D604
          Affiliations
          1CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, 29682 Roscoff, France, 2UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, 29682 Roscoff, France, 3CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France, 4UMR 7138, Université de Nice-Sophia Antipolis, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France, 5Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK, 6Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (EA3882), ESMISAB, Technopôle Brest-Iroise, 29280 Plouzané, France, 7Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain, 8Laboratoire d’Océanographie de Villefranche, Marine Microbial Ecology, UPMC Université Paris 06 et CNRS, UMR7093, Station Zoologique, BP28, 06230 Villefranche-sur-Mer, France, 9Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany, 10Department of Biology, University of Oslo, Marine Biology, NO-0316 Oslo, Norway, 11Department of Genetics and Evolution, University of Geneva, Switzerland, 12Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, 13Laboratory of Soil Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000, Neuchâtel, Switzerland, 14UPMC Université Paris 06, 29682 Roscoff, France, 15CNRS, FR2424, Station Biologique de Roscoff, 29682 Roscoff, France, 16Ifremer, Centre de Brest, DYNECO/Pelagos BP70, 29280 Plouzané, France and 17Point Compétence Informatique, Rue Jean-Baptiste Say, 56850 Caudan, France
          Author notes
          *To whom correspondence should be addressed. Tel: +33 2 98 29 23 79; Fax: +33 2 98 29 23 24; Email: lguillou@ 123456sb-roscoff.fr
          Correspondence may also be addressed to Richard Christen. Tel: +33 6 01 83 01 44; Email: christen@ 123456unice.fr
          Present addresses: Lucie Bittner, Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
          Anne-Laure Sauvadet, School of Biosciences, Cardiff University, Main Building, Cardiff CF10 3AT, UK.
          Article
          gks1160
          10.1093/nar/gks1160
          3531120
          23193267
          538c3d7e-b57c-41ec-9877-a7c52ec37e45
          © The Author(s) 2012. Published by Oxford University Press.

          This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.

          History
          : 14 August 2012
          : 24 October 2012
          : 26 October 2012
          Page count
          Pages: 8
          Categories
          Articles

          Genetics
          Genetics

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