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Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L et al.. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res 41: D597-D604

CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, 29682 Roscoff, France, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, 29682 Roscoff, France, CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France, UMR 7138, Université de Nice-Sophia Antipolis, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (EA3882), ESMISAB, Technopôle Brest-Iroise, 29280 Plouzané, France, Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain, Laboratoire d'Océanographie de Villefranche, Marine Microbial Ecology, UPMC Université Paris 06 et CNRS, UMR7093, Station Zoologique, BP28, 06230 Villefranche-sur-Mer, France, Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany, Department of Biology, University of Oslo, Marine Biology, NO-0316 Oslo, Norway, Department of Genetics and Evolution, University of Geneva, Switzerland, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Laboratory of Soil Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000, Neuchâtel, Switzerland, UPMC Université Paris 06, 29682 Roscoff, France, CNRS, FR2424, Station Biologique de Roscoff, 29682 Roscoff, France, Ifremer, Centre de Brest, DYNECO/Pelagos BP70, 29280 Plouzané, France and Point Compétence Informatique, Rue Jean-Baptiste Say, 56850 Caudan, France.
Nucleic Acids Research (Impact Factor: 9.11). 11/2012; 41(Database issue). DOI: 10.1093/nar/gks1160
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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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    • "Because of their extreme morphological and behavioural diversity, the study of even relatively narrow lineages requires a high degree of taxonomic expertise (e.g. Guillou et al. 2012; Pawlowski and Holzmann, 2014). As a result, the knowledge of protistan ecology and evolution is limited by the small number of taxonomists, resulting in scarcity of taxonomically well-resolved ecological data. "
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    • "For the 'Super-group', 'Phylum' and 'Class' levels, the taxonomic framework of PhytoREF was derived from the PR2 database (http://ssu-rrna.org/; Guillou et al. 2013), which mainly follows a comprehensive recent classification framework of eukaryotes (Adl et al. 2012). The 'Family' and 'Order' levels of terrestrial, marine and freshwater micro-and macroalgae were based on the taxonomic classification system of the AlgaeBase database (Guiry & Guiry 2014; Guiry et al. 2014; http:// www.algaebase.org/). "
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    • "SSU rRNA gene sequences assembled via Cufflinks and those reconstructed with EMIRGE were classified using the Ribosome Database Project web server with an 80% cutoff for the lowest classification level (Wang et al., 2007). Unclassified sequences (generally Eukaryotic) were searched against the SILVA database (Pruesse et al., 2012), the Protist Ribosomal Reference Database (Guillou et al., 2013) and the non-redundant NCBI database using BLASTN. All sequences were then aligned using the SINA Aligner (Pruesse et al., 2012). "
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