EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity

Abstract

AbstractEukRibo is a manually curated, public reference database of small-subunit ribosomal RNA gene (18S rDNA) sequences of eukaryotes, specifically aimed at taxonomic annotation of high-throughput metabarcoding datasets. Unlike other reference databases of ribosomal genes, it is not meant to exhaustively capture all publicly available 18S rDNA sequences from the INSDC repositories, but to represent a subset of highly trustable sequences covering the whole known diversity of eukaryotes. EukRibo strives to include only sequences with verified, up-to-date taxonomic identifications, with a strong focus on protists, and relatively low genetic redundancy, to keep the database compact yet comprehensive. Environmental clone sequences representing previously identified novel diversity are accepted as reference sequences only if they have a precise lineage designation, useful for taxonomic annotation. EukRibo is part of a suite of public resources generated by the UniEuk project, which all follow a common taxonomic framework for maximal interoperability. The high level of taxonomic accuracy of EukRibo allows higher confidence in the taxonomic annotation of environmental metabarcodes, and should facilitate identification of new eukaryotic diversity at various taxonomic levels. The database is currently in version 2, and all versions are permanently stored and made available via the FAIR open platform Zenodo. It is our hope that EukRibo will help ongoing curation efforts of other 18S rDNA reference databases, and we welcome suggestions of corrections and new features to be included in subsequent versions.