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

Type Article
Date 2013-01
Language English
Author(s) Guillou Laure1, 2, Bachar Dipankar3, 4, Audic S1, 2, Bass David5, Berney Cedric5, Bittner Lucie1, 2, Boutte Christophe1, 2, Burgaud Gaetan6, De Vargas Colomban1, 2, Decelle Johan1, 2, Del Campo Javier7, Dolan John R.8, 9, Dunthorn Micah10, Edvardsen Bente11, Holzmann Maria12, Kooistra Wiebe H. C. F.13, Lara Enrique14, Le Bescot Noan1, 2, Logares Ramiro7, Mahe F1, 2, Massana Ramon7, Montresor Marina13, Morard Raphael1, 2, Not Fabrice1, 2, Pawlowski Jan12, Probert Ian15, Sauvadet Anne-Laure1, 2, Siano Raffaele16, Stoeck Thorsten10, Vaulot Daniel1, 2, Zimmermann Pascal17, Christen Richard3, 4
Affiliation(s) 1 : CNRS, UMR Adaptat & Divers Milieu Marin 7144, F-29682 Roscoff, France.
2 : Univ Paris 06, UMR 7144, Stn Biol Roscoff, F-29682 Roscoff, France.
3 : CNRS, UMR 7138, F-06108 Nice 02, France.
4 : Univ Nice Sophia Antipolis, UMR 7138, F-06108 Nice 02, France.
5 : Nat Hist Museum, Dept Life Sci, London SW7 5BD, England.
6 : ESMISAB, Lab Univ Biodivers & Ecol Microbienne EA3882, F-29280 Plouzane, France.
7 : CSIC, Inst Ciencies Mar, Dept Marine Biol & Oceanog, Barcelona, Catalonia, Spain.
8 : Univ Paris 06, Lab Oceanog Villefranche, F-06230 Villefranche Sur Mer, France.
9 : CNRS, UMR7093, Stn Zool, F-06230 Villefranche Sur Mer, France.
10 : Univ Kaiserslautern, Dept Ecol, D-67663 Kaiserslautern, Germany.
11 : Univ Oslo, Dept Biol, NO-0316 Oslo, Norway.
12 : Univ Geneva, Dept Genet & Evolut, CH-1211 Geneva 4, Switzerland.
13 : Stn Zool Anton Dohrn, I-80121 Naples, Italy.
14 : Univ Neuchatel, Lab Soil Biol, CH-2000 Neuchatel, Switzerland.
15 : CNRS, FR2424, Stn Biol Roscoff, F-29682 Roscoff, France.
16 : IFREMER, Ctr Brest, F-29280 Plouzane, France.
17 : Point Competence Informat, F-56850 Caudan, France.
Source Nucleic Acids Research (0305-1048) (Oxford Univ Press), 2013-01 , Vol. 41 , N. D1 , P. D597-D604
DOI 10.1093/nar/gks1160
WOS© Times Cited 434
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 (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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Guillou Laure, Bachar Dipankar, Audic S, Bass David, Berney Cedric, Bittner Lucie, Boutte Christophe, Burgaud Gaetan, De Vargas Colomban, Decelle Johan, Del Campo Javier, Dolan John R., Dunthorn Micah, Edvardsen Bente, Holzmann Maria, Kooistra Wiebe H. C. F., Lara Enrique, Le Bescot Noan, Logares Ramiro, Mahe F, Massana Ramon, Montresor Marina, Morard Raphael, Not Fabrice, Pawlowski Jan, Probert Ian, Sauvadet Anne-Laure, Siano Raffaele, Stoeck Thorsten, Vaulot Daniel, Zimmermann Pascal, Christen Richard (2013). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41(D1), D597-D604. Publisher's official version : https://doi.org/10.1093/nar/gks1160 , Open Access version : https://archimer.ifremer.fr/doc/00114/22492/