title: Robust markers reflecting phylogeny and taxonomy of rhizobia.
abstract: 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 (SMc00019-truA-thrA) 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 (SMc00019-truA-thrA) provided a criterion for bacterial species definition and confirmed 621/629 of known interspecies relationships within Bradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium. Some widely studied strains should be renamed. The SMc00019-truA-thrA ANI also correlates well with the genomic ANI of strains in Agrobacterium, Methylobacterium, Ralstonia, Rhodopseudomonas, Cupriavidus and Burkholderia, suggesting their wide applicability in other bacteria.
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
authors.forename: Yan Ming
authors.initials: YM
authors.lastname: Zhang
authors.forename: Chang Fu
authors.initials: CF
authors.lastname: Tian
authors.forename: Xin Hua
authors.initials: XH
authors.lastname: Sui
authors.forename: Wen Feng
authors.initials: WF
authors.lastname: Chen
authors.forename: Wen Xin
authors.initials: WX
authors.lastname: Chen
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D007887:Fabaceae / Q000382:microbiology; D005819:Genetic Markers / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D009586:Nitrogen Fixation; D010802:Phylogeny; D012988:Soil Microbiology; D013559:Symbiosis
chemical_list: D005819:Genetic Markers