Databases

GreenGenes. The 16S rRNA Database and tools.

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology 72: 5069-5072 doi: 10.1128/AEM.03006-05 [PMDI: 16820507]

ITS2. Internal Transcriber Spacer 2 Ribosomal DNA Database.

Koetschan C, Hackl T, Müller T, Wolf M, Förster F, Schultz J. 2012. ITS2 database IV: Interactive taxon sampling for internal transcribed spacer 2 based phylogenies. Molecular Phylogenetics and Evolution 63: 585-588 doi: 10.1016/j.ympev.2012.01.026 [PMID: 22366368]

RDP. The Ribosomal Database Project.

The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.

Cole JR., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research 42 (D1) D633-D642; doi: 10.1093/nar/gkt1244 [PMID: 24288368]

PR2. Protist Ribosomal Reference Database.

The Protist Ribosomal Reference Database provides an access to unicellular eukaryotes Small SubUnit rRNA and rDNA sequences with curated taxonomy. The database is focused on nuclear-encoded sequences of protists. However, Metazoa, land plants and macrosporic fungi, as well as eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for Next Generation Sequencing dataset analyses. The PR2 database can be downloaded or searched by similarity as explained below. Because of their tremendous diversity, taxonomy of protists is still under progress.

Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C,  Burgaud G, de Vargas C, Decelle J, del Campo J, Dolan JR, Dunthorn M, Bente Edvardsen, Maria Holzmann M, Kooistra WHCF, Lara E, Le Bescot N, Logares R, Mahe F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy.  Nucleic Acids Research 41 (D1) D597-D604. doi: 10.1093/nar/gks1160 [PMID: 23193267]

 SILVA. High quality ribosomal RNA databases.

A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data. SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41 (D1) doi: 10.1093/nar/gks1219 [PMID: 23193283]

PhytoREF. A new reference database of the plastidial 16S rRNA gene of eukaryotes.

The PhytoREF database provides an access to plastidial 16S rRNA gene sequences of a large diversity of photosynthetic eukaryotes with curated and normalized taxonomy. PhytoREF has been built using the publicly available sequences and plastidial genomes from GenBank, as well as, new amplicon sequences obtained from numerous cultures of marine phytoplankton. Stringent quality filtering and phylogeny-based taxonomic classification were applied for each single 16S rRNA gene sequence. All the major eukaryotic lineages that perform photosynthesis or keep a relict plastid are represented in PhytoREF, and comprise terrestrial, freshwater and marine taxa (land plants, marine and freshwater macro and microalgae).

Decelle J, Romac S, Stern RF, Bendif EM, Zingone A, Audic S, Guiry MD, Guillou L, Tessier D, Le Gall F, Gourvil P, Dos Santos AL, Probert I, Vaulot D, de Vargas C, Christen R. 2015. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.  Molecular Ecology Resources doi: 10.1111/1755-0998.12401 [PMID: 25740460]

PFR². A curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.

The PFR² database offers access to planktonic Foraminifera 18S ribosomal DNA sequence library with a curated taxonomy at the morphological and cryptic species level. The sequences have been exclusively obtained by single-cell DNA extraction of taxonomically identify specimens and are associated with metadata. A strict control of the quality of the sequences has been applied and the taxonomy has been curated to achieve full internal consistency. The aim of PFR² is to provide a comprehensive and high quality free resource to study the ecology and biogeography of planktonic foraminifera as a model system for evolution in the pelagic realm. PFR² can be used to annotate environmental sequences and also to design probes and primers.

Morard R, Darling KF, Mahé,F, Audic S, Ujiié Y, Weiner AKM, André A, Seears HA, Wade CM, Quillévéré F, Douady CJ, Escarguel G, de Garidel-Thoron T, Siccha M, Kucera M, de Vargas C. 2015. PFR2 : a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution. Molecular Ecology Resources. 15: 1472–1485. doi:10.1111/1755-0998.12410 [PMID: 25828689]