EukRef-excavates: seven curated SSU ribosomal RNA gene databases

Area of Science:

• Microbial Ecology
• Molecular Biology
• Protistology

Background:

• Small subunit ribosomal RNA (SSU rRNA) gene sequencing is standard for microbial diversity studies.
• Accurate classification of SSU rRNA data requires well-curated reference databases.
• Such databases are lacking for most eukaryotic groups, particularly protists.

Purpose of the Study:

• To address the lack of curated eukaryotic reference databases by the EukRef project.
• To generate well-curated SSU rRNA gene databases for excavate protists.
• To provide reliable standards for excavate identification in ecological studies.

Main Methods:

• Identification and curation of 6121 SSU rRNA gene sequences for excavates.
• Inclusion of sequences from cultures, cell isolations, enrichments, and environmental samples.
• Phylogenetic analysis and classification correction for the curated dataset.

Main Results:

• Development of EukRef-curated databases for excavate protists.
• Correction of classifications for a majority of the curated sequences.
• Creation of a publicly available resource for excavate diversity.

Conclusions:

• The new databases offer phylogenetically based standards for excavate identification.
• Improved accuracy in ecological and microbiome studies involving excavates.
• Facilitation of the classification of newly discovered excavate taxa.