robust markers reflecting phylogeny and taxonomy of rhizobia健壮的标记反映发展史和根瘤菌的分类.pdfVIP

Robust Markers Reflecting Phylogeny and Taxonomy of Rhizobia Yan Ming Zhang1,2,3, Chang Fu Tian1,2,3*, Xin Hua Sui1,2,3, Wen Feng Chen1,2,3, Wen Xin Chen1,2,3 1 State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China, 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China, 3 Rhizobium Research Center, China Agricultural University, Beijing, China 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. Citation: Zhang YM, Tian CF, Sui XH, Chen WF, Chen WX (2012) Robust Markers Reflecting Phylogeny and Taxonomy of Rhizobia. PLoS ONE 7(9): e44936. doi:10.1371/journal.pone.0044936 Editor: Jonathan H. Badger, J. Craig Venter Institute, United States of America Received May 21, 2