Published October 26, 2012 | Version v1
Journal article Open

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Creators

  • 1. CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, 29682 Roscoff, France and UPMC Universite´ Paris 06, UMR 7144, Station Biologique de Roscoff, 29682 Roscoff, France,
  • 2. CNRS, UMR 7138, Syste´ matique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France and UMR 7138, Universite´ de Nice-Sophia Antipolis, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France
  • 3. Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK,
  • 4. Laboratoire Universitaire de Biodiversite´ et Ecologie Microbienne (EA3882), ESMISAB, Technopoˆ le Brest-Iroise, 29280 Plouzane´ , France
  • 5. UPMC Universite´ Paris 06, UMR 7144, Station Biologique de Roscoff, 29682 Roscoff, France,
  • 6. Department of Marine Biology and Oceanography, Institut de Cie` ncies del Mar (CSIC), Barcelona, Catalonia, Spain
  • 7. Laboratoire d’Oce´ anographie de Villefranche, Marine Microbial Ecology, UPMC Universite´ Paris 06 et CNRS, UMR7093, Station Zoologique, BP28, 06230 Villefranche-sur-Mer, France
  • 8. 9Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
  • 9. Department of Biology, University of Oslo, Marine Biology, NO-0316 Oslo, Norway
  • 10. Department of Genetics and Evolution, University of Geneva, Switzerland
  • 11. Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
  • 12. Laboratory of Soil Biology, University of Neuchaˆ tel, Rue Emile Argand 11, CH-2000, Neuchaˆ tel, Switzerland
  • 13. UPMC Université Paris 06, 29682 Roscoff, France and CNRS, FR2424, Station Biologique de Roscoff, 29682 Roscoff, France
  • 14. Ifremer, Centre de Brest, DYNECO/Pelagos BP70, 29280 Plouzane´ , France
  • 15. Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
  • 16. Point Compe´ tence Informatique, Rue Jean-Baptiste Say, 56850 Caudan, France
  • 17. CNRS, 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

Description

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 (PR2, http://ssurrna.
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 hightroughput
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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Additional details

Funding

European Commission
MICRO B3 - Marine Microbial Biodiversity, Bioinformatics and Biotechnology 287589