DinoREF: A Curated Dinoflagellate 18S rRNA Gene Reference Database

A curated reference database of 18S rRNA gene sequences for dinoflagellates (Dinophyceae), compiled by Solenn Mordret and colleagues. The dataset includes sequences from GenBank and literature sources, with multiple taxonomy files and lists of unique V4 regions and OTUs. The associated paper was under revision in 2018.

Use Cases

• Taxonomic classification of dinoflagellate sequences based on the provided 8-level taxonomy files.
• Phylogenetic analysis of dinoflagellate relationships using the curated 18S rRNA gene sequences.
• Design and validation of PCR primers for dinoflagellate detection based on the list of unique V4 sequences.
• Clustering and operational taxonomic unit (OTU) analysis using the provided 98% similarity OTU list.

Strengths

• Includes multiple curated taxonomy files providing classifications at different levels (GenBank, 8-level, Superclades).
• Contains a list of unique V4 sequences, which is useful for primer design and metabarcoding studies.
• Provides OTU clustering information at 98% similarity, aiding in diversity analyses.

Limitations

• Row count and dataset size are unknown, which may limit suitability assessment for large-scale projects.
• Column-level documentation is absent; field semantics must be inferred from the provided 'read-me' file after download.
• Last update date is unknown; the data is associated with a paper under revision in 2018, so freshness is unverified.

Provenance

Source

GenBank and literature sources, as cited in the description.

Collection Method

Curated compilation and annotation of existing public sequences.