Protists Ribosomal Reference Database

Protists Ribosomal Reference Database provides a curated reference of 18S rRNA sequences with taxonomic annotations to support environmental metabarcoding and taxonomic assignment of protists and related taxa.

Key Features:

• Taxonomic Coverage: Contains over 240,000 sequences with annotations across nine taxonomic fields from domain to species level.
• Nuclear-encoded Sequences: Includes 136,866 nuclear-encoded sequences.
• Organelle Sequences: Includes 45,708 organelle sequences, of which 36,501 are mitochondrial and 9,657 are chloroplastic.
• Diverse Taxa: Focuses on protists and also encompasses metazoa, fungi, plants, and a limited set of 16S sequences from plastids and bacteria.
• Metadata Availability: Many sequences include metadata such as geo-localisation, origin (culture or natural sample), and host type.
• Expert Annotation: Annotations are performed by taxonomic experts for each group.
• Chimeric Sequence Curation: Includes a subset of putative chimeric sequences that have been checked.
• Normalized Taxonomy: Provides a normalized eight-term ranked taxonomy for precise taxonomic assignments.
• Sequence Clustering: Offers representative sequences derived by clustering at specified similarity levels.

Scientific Applications:

• Environmental Metabarcoding: Provides curated 18S rRNA references to support environmental metabarcoding analyses.
• Taxonomic Assignment: Enables taxonomic assignment of protists and related taxa using annotated 18S rRNA and rDNA sequences.
• Organelle Sequence Analysis: Supports detection and characterization of mitochondrial and chloroplastic sequences and available 16S plastid/bacterial sequences.
• Chimera Detection and Quality Control: Aids identification and curation of putative chimeric sequences within sequence datasets.
• rRNA/rDNA and Intron Studies: Supports analyses of rRNA and rDNA sequences, including introns relevant to eukaryotic studies.

Methodology:

Uses sequence similarity searches, clustering at specified similarity levels to produce representative sequences, and checking/flagging of putative chimeric sequences.