Assembling the largest 18S ribosomal RNA curated data set for non-bilaterian animals

Abstract

The small subunit ribosomal RNA (SSU rRNA), named 18S in eukaryotes, is a gene universally present in all branches of the Tree of Life that has been instrumental to solve the most ancient relationships. Furthermore, it serves as a molecular identifier of biodiversity in environmental DNA studies. Despite its significance, specialised 18S databases still contain errors and struggle to keep pace with the rapidly changing eukaryotic taxonomy and the influx of novel diversity. This challenge hinders the assembly of reliable reference phylogenetic trees needed to identify novel 18S sequences obtained through metabarcoding studies. As part of a larger project aimed at creating reference databases for eukaryotic 18S (EukRef), this work focuses on curating the 18S sequences of non-bilaterian animals (sponges, ctenophores, cnidarians and placozoans) in the Protist Ribosomal Reference Database (PR2). Through this curation process, we generated the largest backbone phylogenetic tree for non-bilaterians, essential for the taxonomic identification of 18S sequences within this group. Furthermore, we reaffirmed that 18S is a suitable phylogenetic marker for animals, as it can recover most well-known clades to the phylum level. Lastly, we confirmed that incorporating 18S secondary structure information into sequence alignment positively impacts the topology of the inferred animal Tree of Life.