About PR2

The eukaryotic tree. From Burki et al. 2019. The New Tree of Eukaryotes. Trends in Ecology & Evolution. DOI: 10.1016/j.tree.2019.08.008.

Current version : 4.12.0
Last update : 8 August 2019
DOI : 10.6084/m9.figshare.5913181

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.

Representation of the different taxonomic groups within PR2.

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

Get the PR2 database

PR2 sequence database

The PR2 database is provided in 3 different formats:

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

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

PR2 primer database

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

Documentation

Presentation of the PR2 database

Structure of the PR2 database

Data provided

Management and revision history

Tutorials

Tutorials

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

Contributing

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.

The PR2 Team

Core team

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Javier del Campo

U. Miami, USA

Microbial Ecology and Evolution

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Daniel Vaulot

NTU, Singapore

Marine Phytoplankton

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Laure Guillou

CNRS, France

Marine parasites

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Frédéric Mahé

CIRAD, France

Bioinformatics

Scientific Committee

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Fabien Burki

Uppsala U., Sweden

Tree of eukaryotes, phylogenomics, metabarcoding, long-reads, protists, diversity

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Bente Edvardsen

U. Oslo, Norway

Haptophyta

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Martin Kolísko

CAS, Czech Republic

Apicomplexa

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Ramon Massana

ICM, Spain

Stramenopiles

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Fabrice Not

CNRS, France

Radiolaria

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Laura Parfrey

UBC, Canada

Protists

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Luciana Santoferrara

U. Connecticut, USA

Ciliates

Funding