PR2 — A reference 18S rRNA sequence database

Wed, 27 Apr 2016 00:00:00 +0000

The PR2 database was initiated in 2010 in the frame of the BioMarks project, building on work developed over the previous decade in the Plankton Group at the Station Biologique de Roscoff. Its aim is to provide a reference database of carefully annotated 18S rRNA sequences using eight unique taxonomic fields (from kingdom to species). It currently contains over 184,000 sequences, with metadata fields including geo-localisation, culture or environmental origin, host type, and more.

Annotation of PR2 is performed by experts from each taxonomic group. An important partner in this effort is EukRef, which has merged its bioinformatics pipelines and workshop-based curation efforts with PR2. EukRef has built tools used during multiple workshops dedicated to specific taxonomic groups, including ciliates, choanoflagellates, and others.

Key publications

Laure Guillou et al. (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 et al. (2018). EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology.

Issues and contributions

Report issues or contribute on GitHub.

Database | del Campo Lab - Microbial Ecology and Evolution

PR2 — A reference 18S rRNA sequence database