Protist Ribosomal Reference database (PR²)

SSU rRNA gene database

The Protist Ribosomal Reference database (PR²) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.

Since the original web site (http://ssu-rrna.org/pr2) does not exist any more, we are proposing updated version of PR² and provide the data in a variety of file formats to use for annotating metabarcodes.

Current version

• Current version : 4.11.1
• Last update : 13 December 2018
• DOI : https://doi.org/10.6084/m9.figshare.5913181
• Manual : https://github.com/pr2database/pr2database/wiki

Downloading the database

• Flat files - latest release

• R package using Devtools

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

Basic statistics

• PR² statistics

Report issues

• Please report any issue on GitHub

Contact

Daniel VAULOT, Laure GUILLOU and Fabrice NOT, ECOMAP team, Plankton Group, UMR 7144 CNRS-UPMC Station Biologique, Place G. Tessier 29680 Roscoff FRANCE email: vaulot@sb-roscoff.fr / vaulot@gmail.com

Contributors

• Tristan Biard (Wimereux Station)
• Margot Tragin (Roscoff)
• Bente Edvardsen (U of Oslo)
• Charles Bachy and Wei Ting Chen (Roscoff)
• Solenn Mordret (Naples)
• Adriana Lopes dos Santos (Nanyang Technological University, Singapore)
• Vittorio Boscaro (UBC, Vancouver) and the EukRef ciliate team

Please cite

• 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.

Related Sites and databases

Eukref (18S annotation)

PR² will be incorporating annotations made by the EukRef project as deposited in their GitHub repository.

PhytoRef (16S plastid)

Plastid 16S rRNA sequences are yet not included into PR². These sequences are available from the the PhytoRef database available from Figshare or PhytoRef.

PFR2 - Foraminifera 18S ribosomal DNA databae

The database offers access to planktonic Foraminifera 18S ribosomal DNA sequence library with a curated taxonomy at the morphological and molecular level. The compilation was facilitated through the efforts of the SCOR/IGBP Working Group 138 “Modern planktonic foraminifera and ocean changes”.

PFR2