Robust markers reflecting phylogeny and taxonomy of rhizobia.

Yan Ming Zhang, Chang Fu Tian, Xin Hua Sui, Wen Feng Chen, Wen Xin Chen

PloS one 2012

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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.

Citation

Yan Ming Zhang, Chang Fu Tian, Xin Hua Sui, Wen Feng Chen, Wen Xin Chen. Robust markers reflecting phylogeny and taxonomy of rhizobia. PloS one. 2012;7(9):e44936