Fig. 1: MAGs from diverse environments expand known and add previously undescribed clades in the phylum Chlamydiae.

a Maximum likelihood phylogenetic tree based on a concatenated set of 43 conserved marker proteins (5704 sites) in which published genomes and 82 MAGs generated in the GEM initiative are shown in black and orange, respectively. Chlamydial monophyly was supported by optimized ultrafast bootstrap and SH likelihood ratio test support with 100% for both. Previously established chlamydial families are shaded in light gray, previously undescribed families are shaded in orange. The tree was inferred under the LG + C60 + G4 + F model with the IQ-TREE software. Nodes with an optimized ultrafast bootstrap support ≥ 95% are labelled with black circles. Tree annotations from inside to outside: (1) completeness, (2) contamination, (3) MAG with 16S rRNA gene, (4) high quality MAGs, (5) environmental origin (white stars indicate genomes from cultured isolates), (6) %GC content, (7) assembly size and estimated genome size (stacked white and gray bars, respectively), and (8) names of chlamydial families represented by more than ten genomes and added metagenomic clades indicated by orange segments. Scale bar indicates 0.1 substitutions per position in the alignment. b Number of MAGs retrieved per environmental category. c Completeness and contamination estimates of chlamydial MAGs from the GEM dataset. Shaded gradients behind the completeness and contamination boxplots represent the values in the heatmap boxes in the tree.