Fig. S7.

Whole-genome comparison and core metabolism of N. moscoviensis and Nitrospira defluvii. (A) Whole-genome alignment showing the positions of homologous genes in N. moscoviensis and N. defluvii. Sequence matches with the same orientation are plotted blue, whereas inversions are plotted red. (B) Localization of regions encoding the Nitrospira core metabolism for nitrite oxidation, electron transport, and inorganic carbon fixation in the genomes of N. defluvii (Left) and N. moscoviensis (Right). Each semicircle depicts one full genome. Ribbons connect regions containing homologous core metabolism genes. Tags (D1 to D23 for N. defluvii, M1 to M28 for N. moscoviensis) identify the genomic regions shown in C–E. (C) Highly conserved, syntenic gene arrangements within regions encoding nitrite oxidoreductase (NXR) in the genomes of N. defluvii (Left) and N. moscoviensis (right). Regions are separated by spaces and ribbons connect homologous genes. The tags, which identify the regions, are the same as in B. The order of the regions shown here facilitates the synteny comparison and does not reflect the true genomic localization of these regions, which is shown in B. (D) Highly conserved, syntenic gene arrangements within regions encoding the electron transport chains for nitrite oxidation, reverse electron transport, and the utilization of organic substrates in the genomes of N. defluvii (Left) and N. moscoviensis (Right). Regions are separated by spaces and ribbons connect homologous genes. The tags, which identify the regions, are the same as in B. The order of the regions shown here facilitates the synteny comparison and does not reflect the true genomic localization of these regions, which is shown in B. (E) Highly conserved, syntenic gene arrangements within regions encoding the reductive (rTCA) and oxidative (oTCA) tricarboxylic acid cycles in the genomes of N. defluvii (Left) and N. moscoviensis (Right). The rTCA cycle is the CO₂ fixation pathway of Nitrospira. Regions are separated by spaces and ribbons connect homologous genes. The tags, which identify the regions, are the same as in B. The order of the regions shown here facilitates the synteny comparison and does not reflect the true genomic localization of these regions, which is shown in B.