Fig. 2

Phylogenetic trees of amoA and amoB in Nitrosomonadales. Double-headed arrows indicate concerted evolution events. Syntenic orthologs are represented by thick branches in the same color in the phylogeny. Flanking genes are denoted by colored bricks, and chromosome segments are denoted by gray bars. Genes involved in the ammonia oxidation pathway (amoA-E) are labeled above the colored bricks. The functions of flanking genes are shown at the bottom. Numbers adjacent to the nodes in the phylogeny are bootstrap percentages obtained from 500 pseudoreplicates. Only bootstrap percentages ≥50 are shown. The name of each operational taxonomic unit is represented by the abbreviation of species name and gene locus. Abbreviations of species names are listed in Supplementary Data 1