Improved taxonomic annotation of Archaea communities using LotuS2, the Genome Taxonomy Database and RNAseq data

Abstract

Metabarcoding is increasingly used to uncover diversity and characterise communities of Archaea In various habitats, but taxonomic annotation of their sequences remains more challenging than for bacteria. Fewer reference sequences are available; widely used databases do not reflect recent revisions of higher level archaeal taxonomy and a substantial fraction of their phylogenetic diversity remains to be fully characterised. We address these gaps with a systematic and tractable approach based around the Genome Taxonomy Database (GTDB). GTDB provides a standardized taxonomy with normalized ranks based on protein coding genes, allowing us to identify and remove incongruent SSU sequences. We then use this in combination with the eukaryote PR2 database to annotate a collection of near full length rRNA sequences and the Archaea SSU sequences in SILVA, creating a new reference database, KSGP (Karst, Silva, GTDB and PR2). GTDB SSUs alone provides a small improvement in annotation of an example marine Archaea OTU data set over standardized SSU databases such as SILVA and Greengenes2, while KSGP increases Class and Order assignments by 145% and 280% respectively and is likely to provide some improvement in annotation of bacterial sequences too. We make the KSGP database and a cleaned and deduplicated subset of GTDB SSU sequences available at ksgp.earlham.ac.uk; integrate them into a metabarcoding pipeline, LotuS2 and outline rapid and robust strategies to generate a set of annotated Archaea OTUs and to determine the proportion of Archaea sequences in metatranscriptomic data. We also demonstrate simple tools to visualise the completeness of database coverage and outline strategies to further understand poorly characterised components of the archaeal community which will be equally applicable to bacteria.