Fig. 1: Phylogenomic tree of Thaumarchaeota.
From: Gene duplication drives genome expansion in a major lineage of Thaumarchaeota
This tree includes 152 thaumarchaeotal genomes (29 culture genomes, 51 single-cell-assembled genomes (SAG) and 72 metagenome-assembled genomes (MAGs), including 12 novel MAGs obtained in this study) from a range of environments and 11 Aigarchaeota genomes and is rooted with two Bathyarchaeota genomes. The tree was inferred by maximum likelihood from 75 concatenated phylogenetic markers, which were aligned separately and analysed using the best-fitting model for each alignment. The 12 new genomes assembled in this study are indicated by red tip labels. Clades that previously lacked representative genomes are indicated with dotted red branches. Dots indicate branches with >95% UFBoot and SH-aLRT support. Coloured order-level clades are further divided into family-level clades with black clade borders. Protein novelty is defined as the percentage of encoded proteins that lack a close homologue (e-value <10−5, % ID >35, alignment length >80 and bit score >100) in the arCOG database. Detailed genome information is given in Supplementary Data 1.
