Current version : 4.12.0
Last update : 8 August 2019

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

Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR²): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597–604.

del Campo J., Kolisko M., Boscaro V., Santoferrara LF., Nenarokov S., Massana R., Guillou L., Simpson A., Berney C., de Vargas C., Brown MW., Keeling PJ., Wegener Parfrey L. 2018. EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology 16:e2005849. DOI: 10.1371/journal.pbio.2005849.

Issues

Report on GitHub

PR2 sequence database

The PR² database is provided in 3 different formats:

Flat files for use with mothur, QIIME2, dada2, blast etc…

• Download latest release
• Details of file provided

R package pr2database

• Use the following code under R

  install.packages(devtools)
  devtools::install_github("pr2database/pr2database")
  

• How to use the R package

SQLite database

• Download

• How to use the SQLite database

PR2 primer database

We are also developing a PR² primer database focusing on the rRNA operon.

• Primers used to amplify 18S rRNA
• Primer sets (fwd/rev) used for metabarcoding of 18S rRNA

Download the PR² database

• As text files
• As an R package
• As a SQLite database

Presentation of the PR² database

• PR² in numbers
• Slide show -2018-11-05

Structure of the PR² database

• Database structure
• Detailed description of the fields

Management and revision history

• Management tools
• Revision history
  • Condensed
  • Detailed
• Major groups recently revised

Tutorials

We are developing small tutorials to make the best use of PR². More will be coming soon…

• Computing some basic statistics
• Plotting geographic location of PR2 sequences

You can contribute to the PR² database in different ways.

• The EukRef project has developed pipelines to obtain sequences from a given phylogenetic group. It organizes workshops focused on specific groups (more information soon on up-coming workshops).
• You can also provide expert annotation or metadata for a taxonomic group you have analyzed in the framework of your thesis or a specific project. See detailed instructions here.