The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

By Laure Guillou, Dipankar Bachar, S. Audic, David Bass, Cédric Berney, L. Bittner, C. Boutte, G. Burgaud, C. de Vargas, J. Decelle and 22 more. Nucleic Acids Res., 2012

2,053 citations recorded by the source corpus.

The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) 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. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/06aacf31c60bc54f189b89861b431f06a545ceb9

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In Ecology

1. K. Deiner
2. F. Altermatt
3. E. Mächler
4. Frédéric Boyer
5. É. Coissac
6. P. Taberlet
7. Aurélie Bonin
8. Peer Bork

In Molecular Biology

1. K. Deiner
2. F. Altermatt
3. E. Mächler
4. Frédéric Boyer
5. Frank Oliver Glöckner
6. Jörg Peplies
7. É. Coissac
8. P. Taberlet

Citations in the corpus

• Determinants of community structure in the global plankton interactome (2015, methodology): “(73); (ii) the experts screened 293 publications”
• Swarm v2: highly-scalable and high-resolution amplicon clustering (2015, methodology): “The PR2 v203 reference database was used for taxonomic assignment (Guillou et al., 2013).”
• Insights into global diatom distribution and diversity in the world’s ocean (2016, background): “Fourtanier and Kociolek (65) have cataloged 900 diatom genera whereas our reference database has only 159 genera (39), indicating that many genera lack sequence information.”
• Metacoder: An R package for visualization and manipulation of community taxonomic diversity data (2016, methodology): “The extract taxonomy function has been used successfully to parse several major database formats including Genbank [10], UNITE [11], Protist Ribosomal Reference Database (PR2) [12], Greengenes [13], Silva [14], and, as illustrated in figure 1, the RDP [9].”
• Microbial colonization of microplastics in the Caribbean Sea (2020, methodology): “Amplicon sequences variants (ASVs) were classified against the Silva (bacteria) and Protist Ribosomal Reference (eukaryotes) (Guillou et al. 2012) databases using trained classifiers.”
• Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion (2018, positive): “Nematode OTUs were taxonomically assigned to genus level against the quality curated PR2 database (Guillou et al., 2013), while sub- genus level classification was treated as OTUs.”
• Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, background): “…databases exist featuring many of the commonly used microbial taxonomic markers for prokaryotes (Cole et al., 2009), microbial eukaryotes (Guillou et al., 2013; Pruesse et al., 2007; Quast et al., 2012) and fungi (Abarenkov et al., 2010), meaning that microbial data sets can be analysed…”
• Eukaryotic plankton diversity in the sunlit ocean (2015, methodology): “This database derives from the Protist Ribosomal Reference (PR2) database (69) but focuses on the V9 region of the”
• obitools: a unix‐inspired software package for DNA metabarcoding (2016, methodology): “…(down-loadable at the following URL: ftp://ftp.ncbi.nih.gov/ pub/taxonomy/taxdump.tar.gz) into the OBITOOLS format, two other OBITOOLSOBISILVA and OBIPR 2 are dedicated to reformat the SILVA (Pruesse et al. 2007) and PR 2 (Guillou et al. 2013) databases into the OBITOOLS format, respectively.”
• The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks (2013, background): “These complications plus the fact that protists are infrequently included in microbial ecology studies (28) are most likely the reasons for SILVA being unique in its inclusion of sequences and taxonomies of all three domains of life, although a curated database dedicated exclusively to eukaryotic se”