Fig. 2: Gene distribution and pathway overview in the Azoamicaceae genomes.
a UpSet plot showing the coding sequence (CDS) content shared between, or unique to, the individual Azoamicaceae genomes. Each vertical bar represents the number of genes in an intersecting set between the genomes. The filled circles connected by lines indicate which genomes contribute genes to the intersecting set. Sets are ordered by the number of genomes contributing, and then the number of genes in the set. Vertical bars are colored according to the broad classification of genes that can be found in Supplementary Data 2. Total coding sequence numbers for the genomes are Ca. A aquiferis 352; Ca. A agrarius 347; Ca. A soli 299; Ca. A ciliaticola 311; Ca. A viridis 378 (b, inset) Distribution of the gene content shown in panel A, summarized by genus. Aa: Azoamicus, As: Azosocius. (c, inset) Distribution of the CDS content shown in panel A summarized by the number of genomes containing each gene. (d) Key pathways in the Azoamicaceae genomes that could enable generation of ATP for the host cell from both denitrification and aerobic respiration. Boxes indicate protein complexes or pathways, with background shading corresponding to the categories in panels (a–c). Filled and empty circles indicate the presence/absence of a complex or pathway in the genome. Roman numerals in the boxes representing the electron transport chain complexes indicate: (I) NADH dehydrogenase, (II) succinate dehydrogenase, (III) bc1 complex, (IV) cytochrome cbb3 oxidase, (V) ATP synthase.
