Robust Markers Reflecting Phylogeny and Taxonomy of Rhizobia

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

doi:10.1371/journal.pone.0044936

Yan Ming Zhang, Wen Feng Chen + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0044936

Copy DOI

Journal: PloS one	Publication Date: Sep 17, 2012
Citations: 88	License type: CC BY 4.0

Affiliation: China Agricultural University

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.

Highlights

Theory-based concepts of prokaryotic species have been debated in the community [1] but, pragmatically, prokaryotic species have been defined by polyphasic approaches including phenotypic and genetic methods
Average nucleotide identity (ANI) analysis ANI between genomes (ANIm) was calculated by using the NUCmer algorithm [14] integrated in Jspecies [4].The ‘‘No of differences’’ model integrated in MEGA 5 [15] was used for calculating the pairwise distance between sequences of a single gene, from which ANI values (ANIg) were obtained using Excel
Consistent with the genomic ANIm 95%–96% boundary for the species definition of other prokaryotes, it was recently shown that genomic ANIm .95% could be used to identify strains of the same rhizobial species [4,13]

Summary

Introduction

Theory-based concepts of prokaryotic species have been debated in the community [1] but, pragmatically, prokaryotic species have been defined by polyphasic approaches including phenotypic and genetic methods. The 70% DDH criterion does not correspond to an ecological/ evolutionary theory-based concept of what properties a species should have [3]. The advance of sequencing technology has allowed us to use comparative genomics and multi-locus sequence analysis (MLSA) to provide a closer marriage between the definition and concept of species [3]. In a phylogenetic and/or taxonomic survey, it is unnecessary to sequence genomes for all the prokaryotes under study and genome assembly may not even be possible, as in metagenomics. The species- and subspecieslevel analyses dominated the topics of most studies and are increasingly important in microbiome survey [8,9]

Methods

Results

Conclusion