Appendix 11—figure 1. Phylogenomic exploration of the unknown sequence space in Archaea.

(A) Distribution of the lineage-specific gene clusters by taxonomic level. Lineage-specific unknown gene clusters are more abundant at the lower taxonomic levels (genus, species). (B) Phylogenetic conservation of the known and unknown sequence space in 1,569 archaeal genomes from GTDB. We calculated the mean trait depth (add symbol _D) with the consenTRAIT algorithm and the lineage specificity using the F1-score approach from Mendler et al., 2019. We observe differences in the conservation between the known and the unknown sequence space for lineage- and non-lineage-specific gene clusters (paired Wilcoxon rank-sum test; all P-values <  0.0001). (C) The majority of the lineage-specific clusters are part of the unknown sequence space, being a small proportion found in prophages present in the GTDB genomes. (D) Known and unknown sequence space of the 1,569 GTDB archaeal genomes grouped by archaeal phyla. Phyla are partitioned based on the ratio of known to unknown gene clusters and vice versa from the set of genomes. Phyla enriched in Metagenomic assembled genomes (MAGs) have a higher proportion in gene clusters of unknown function.