The PR² (Protist Ribosomal Reference) database ecosystem is a set of three interconnected 18S rRNA databases that are useful in particular for metabarcoding applications.

PR² reference sequence database

• Current version : 5.1.0
  
• Last update : 02 April 2025
• Web interface - https://app.pr2-database.org
  
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• Download files: https://github.com/pr2database/pr2database/releases
• R package
• Contributors

The PR² reference sequence 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 nine unique taxonomic fields (from domain to species). At present it contains over 220,000 sequences. Although it focuses on protists, it also contains sequences from metazoa, fungi and plants as well a limited set of 16S sequences from plastids and bacteria. 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 important project in this respect is EukRef which is now part of 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. Now the PR² web interface provides also access to the ROD database that contains full-length eukaryotic ribosomal operons. The database is based on the genome assemblies from NCBI, and the operons are extracted from the assemblies. The database currently contains 69,480 operon variants from more than 11,935 genomes.

PR² primer database

• Current version : 2.0.0
  
• Last update : 15 April 2023
• Web interface: https://app.pr2-primers.org
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• Contributors

We have developed an interactive pr2-primers database focusing on the rRNA operon. You can download primer and primer sets. Primer pairs are evaluated against the PR² sequence database and you can test your own primers and primer sets. To know more.

metaPR² metabarcodes database

• Current version : 2.1.0
• Last update : 16 May 2023
• Web interface: https://app.metapr2.org
  
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• R package
• Contributors

The metaPR² database contains processed 18S rRNA metabarcodes that are annotated with the PR² reference sequence database. Version 1.1 of the database contains 41 datasets corresponding to more than 4,000 samples and 90,000 ASVs. The database is accessible through both a web-based interface (https://app.metapr2.org) and an R package. To know more.

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.

• Vaulot, D., Mahé, F., Bass, D., & Geisen, S. (2021). pr2-primer : An 18S rRNA primer database for protists. Molecular Ecology Resources. DOI: 10.¹¹¹¹⁄₁₇₅₅-0998.13465

• Vaulot, D., Sim, C.W.H., Ong, D., Teo, B., Biwer, C., Jamy, M., Lopes dos Santos, A., 2022. metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources. DOI: 10.¹¹¹¹⁄₁₇₅₅-0998.13674

• Krabberød, A.K., Stokke, E., Thoen, E., Skrede, I. & Kauserud, H. 2025. The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies. Molecular Ecology Resources. 25:e14031.

Issues and questions

• Report on GitHub

PR2 reference sequence database

• Three different formats are provided:
  
  • Web interface
  • Flat files for use with mothur, QIIME2, dada2, blast etc…
  • R package
• Previous versions
• Revision history

PR2 primer database

• Interactive web site
• Code repository

metaR2 metabarcode database

• Interactive web site
• R package
• Code repository

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.