EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.

Area of Science:

• Molecular biology
• Eukaryotic diversity
• Bioinformatics

Background:

• Nuclear ribosomal RNA (rRNA) markers are crucial for molecular identification of micro- and macroorganisms.
• Research on eukaryotic diversity in global ecosystems relies heavily on these nuclear rRNA markers.
• Existing databases often lack comprehensive coverage across all eukaryotic groups or rRNA markers.

Purpose of the Study:

• To present EUKARYOME, a community-curated reference database for nuclear rRNA markers (18S, ITS, 28S) covering all eukaryotes.
• To provide a comprehensive resource particularly useful for identifying arbuscular mycorrhizal fungi.
• To offer long-read sequences for advanced taxonomic identification and chimera control in high-throughput sequencing.

Main Methods:

• Database curation by the research community.
• Inclusion of nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS), and 28S rRNA markers.
• Incorporation of reference long-read sequences from (meta)genomic and (meta)barcoding data.
• Taxonomic assignments verified using phylogenetic approaches.

Main Results:

• EUKARYOME provides a unified reference database for all eukaryotes, encompassing metazoans, protists, fungi, and plants.
• The database integrates four commonly used molecular markers (ITS1, ITS2, 18S V4-V5, 28S D1-D2) for enhanced identification, especially for arbuscular mycorrhizal fungi.
• It includes unique long-read sequences beneficial for third-generation sequencing data analysis and chimera detection.

Conclusions:

• EUKARYOME significantly advances eukaryotic molecular identification by offering a comprehensive, non-restricted, and multi-marker reference database.
• The database supports diverse research applications, from broad eukaryotic diversity studies to specific fungal identification and advanced sequencing analyses.
• Availability of curated datasets promotes standardized and accurate molecular identification across the eukaryotic domain.