Skip to main content
ARS Home » Research » Publications at this Location » Publication #164228


item Van Berkum, Peter

Submitted to: North American Conference on Symbiotic Nitrogen Fixation
Publication Type: Abstract Only
Publication Acceptance Date: 6/27/2004
Publication Date: 6/27/2004
Citation: Van Berkum, P.B., Eardly, B.B. 2004. Genomes, ribosomal genes and evolutinary biology of rhizobia [abstract]. North American Conference on Symbiotic Nitrogen Fixation.Program and Abstracts. P.19.

Interpretive Summary:

Technical Abstract: For little more than a decade now it has been the practice to portray the evolutionary relationships among bacterial genomes by variability in 16S rRNA gene sequences. Besides estimating hierarchical relationships among genomes to reconstruct phylogeny, these data also are predominant in their use to support proposals in bacterial taxonomy. However, it is becoming quite apparent that using variability in ribosomal gene sequences to represent hierarchies among bacterial genomes may be inappropriate. This in turn has become an issue in taxonomy. The question for concern originates from a lack of evidence for hierarchy among 16S rRNA gene sequences. This is coupled with the continued increase in data from detailed scrutiny of polymorphic base distribution that supports an inference implying that a reticulate evolutionary process formed the extant alleles. Obviously, in view of this conclusion it would be incorrect to predict common ancestry between two genomes from a phylogenetic tree of 16S rRNA gene sequences where sequence variation exists in part because of recombination between divergent alleles. Since it would be impossible to justify using the 16S rRNA gene to represent genetic relationships among genomes an alternative approach is required. From the published complete genome sequence of R. meliloti strain 1021 it is possible to select loci that are distributed across each replicon for use in multilocus sequence typing (MLST). The resulting data can be used for determining genetic variability and to search for genetic recombination.