Fig. 1: Phylogenomic trees and gene content of Nitrospirota and Nitrospinota phyla, showing distinct clades and gene clusters associated with basal groups comprised mainly of subsurface organisms (purple bar at bottom) or later-branching groups (green bars at bottom). | The ISME Journal

Fig. 1: Phylogenomic trees and gene content of Nitrospirota and Nitrospinota phyla, showing distinct clades and gene clusters associated with basal groups comprised mainly of subsurface organisms (purple bar at bottom) or later-branching groups (green bars at bottom).

From: Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

Fig. 1

The trees are oriented so the middle of the image contains the outgroups for both trees. Phylogenetic trees were produced used the Bac120 marker set (min 12 genes) using the PhyloPhlan pipeline to create the alignments and IQ-TREE using the LG + F + G4 model chosen by ModelFinder using the Bayesian Information Criterion (BIC) and 1000 ultra-fast non-parametric bootstraps. Heatmaps of gene cluster absence (empty) or present in at least 10% of the genomes in the given phyla (filled) are displayed below the trees. Rows of gene clusters are ordered by hierarchical clustering using wards linkage. Blocks of genes enriched in the Nitrospinia or Nitrospiria are highlighted with the green boxes, and purple used to highlight the enriched gene clusters in the basal classes of the given phyla. Hierarchical clustering of genomes solely by gene content produced similar groupings as the phylogenies (Supplementary Figure 5).

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