Robust Markers Reflecting Phylogeny and Taxonomy of Rhizobia

<div><p>Genomic ANI (Average Nucleotide Identity) has been found to be able to replace DNA-DNA hybridization in prokaryote taxonomy. The ANI of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ANI. This allowed us to identify three housekeeping genes (<em>SMc00019</em>-<em>truA</em>-<em>thrA</em>) whose ANI reflected the intraspecies and interspecies genomic ANI among rhizobial strains, revealing an ANI gap (≥2%) between the inter- and intra-species comparisons. The intraspecies (96%) and interspecies (94%) ANI boundaries calculated from three genes (<em>SMc00019</em>-<em>truA</em>-<em>thrA</em>) provided a criterion for bacterial species definition and confirmed 621/629 of known interspecies relationships within <em>Bradyrhizobium</em>, <em>Mesorhizobium</em>, <em>Sinorhizobium</em> and <em>Rhizobium</em>. Some widely studied strains should be renamed. The <em>SMc00019</em>-<em>truA</em>-<em>thrA</em> ANI also correlates well with the genomic ANI of strains in <em>Agrobacterium</em>, <em>Methylobacterium</em>, <em>Ralstonia</em>, <em>Rhodopseudomonas</em>, <em>Cupriavidus</em> and <em>Burkholderia</em>, suggesting their wide applicability in other bacteria.</p>