PR2 database. A reference 18S rRNA sequence database

The PR2 database was initiated in 2010 in the frame of the BioMarks project from work that had developed in the previous ten years in the Plankton Group of the Station Biologique of Roscoff. Its aim is to provide a reference database of carefully annotated 18S rRNA sequences using eight unique taxonomic fields (from kingdom to species). At present it contains about 184,000 sequences. A number of metadata fields are available for many sequences, including geo-localisation, whether it originates from a culture or a natural sample, host type etc… The annotation of PR2 is performed by experts from each taxonomic groups. One very important project in this respect is EukRef which has recently decided to merge its effort with PR2. EukRef has built bioinformatics pipelines that have been used during three workshops dedicated to specific taxonomic groups. As an example, part of the ciliate annotation originate from the first EukRef workshop.

Citations

Laure Guillou, Dipankar Bachar, Stéphane Audic, David Bass, Cedric Berney, Lucie Bittner, Christophe Boutte, Gaétan Burgaud, Colomban de Vargas, Johan Decelle, others (2013). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Research.

Javier del Campo, Martin Kolisko, Vittorio Boscaro, Luciana F Santoferrara, Serafim Nenarokov, Ramon Massana, Laure Guillou, Alastair Simpson, Cedric Berney, Colomban de Vargas, others (2018). EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology.

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