The PR2 database ecosystem

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.

The PR2 (Protist Ribosomal Reference) database ecosystem is a set of three interconnected 18S rRNA databases that are useful in particular for metabarcoding applications. This web site focuses on the PR2 reference sequence database.

The PR2 reference sequence database

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 eight unique taxonomic fields (from kingdom to species). At present it contains almost 200,000 sequences. Although it focuses on protists, it also contains sequences from metazoa, fungi and plants as well a limited set 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 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.

The PR2 primer database

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.

The metaPR2 metabarcodes database

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://shiny.metapr2.org) and an R package. To know more.

Citations

Issues and questions

Get the PR2 databases

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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Daniel Vaulot

CNRS, France

PR2 coordinator, metaPR2

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Javier del Campo

U. Miami, USA

PR2 reference, EukRef

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Frédéric Mahé

CIRAD, France

PR2 primers

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Laure Guillou

CNRS, France

PR2 reference

Funding