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
and eukaryotic
organelles (mitochondrion, plastid and others) 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.
The original web site (http://ssu-rrna.org/pr2) is currently out and we are proposing updated version of PR2 as flat files to use for annotating metabarcodes.
Files
The files provided are for use with Qiime or Mothur. Four files are provided. * pr2....fasta contains all sequences in fasta format * pr2....tax contains the taxonomy of each sequence * PR2 version notes.docx contains the revision history * PR2 versions.xls is a condensed list of the different versions
Current version : 4.3 based on GenBank 203
Notes - Qiime can only use 7 taxonomical levels
Contact
Laure GUILLOU and Daniel VAULOT DIPO team, Plankton Group, UMR 7144 CNRS-UPMC Station Biologique, Place G. Tessier 29680 Roscoff FRANCE email: vaulot@sb-roscoff.fr
Contributors
- Tristan Biard - Margot Tragin - Bente Edvardsen
References
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.
Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. Perspect. Phycol. in press.
Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. Perspect. Phycol. in press.