Gene duplication drives genome expansion in Thaumarchaeota

Abstract Ammonia-oxidising archaea of the phylum Thaumarchaeota are keystone species in global nitrogen cycling. However, only three of the six known families of the terrestrially ubiquitous order Nitrososphaerales possess representative genomes. Here we provide genomes for the three remaining families and examine the impact of gene duplication, loss and transfer events across the entire phylum. Much of the genomic divergence in this phylum is driven by gene duplication and loss, but we also detected early lateral gene transfer that introduced considerable proteome novelty. In particular, we identified two large gene transfer events into Nitrososphaerales. The fate of gene families originating on these branches was highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles within soil and sediment environments. Overall, our results suggest that lateral gene transfer followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.