In the past, bacterial phylogeny relied almost exclusively on 16S rRNA gene sequence analysis. More recently, multilocus sequence analysis has been used to infer organismal phylogenies. In this study, the chaperone gene was investigated as a marker for phylogeny studies in alphaproteobacteria. Preliminary analysis of G+C contents and G+C3s contents (the G+C content of the synonymous third codon position) showed no clear evidence of horizontal transfer of this gene in proteobacteria. -based phylogenies were then analysed at three taxonomic levels: the , the and the genus . Dendrograms based on DnaJ and 16S rRNA gene sequences revealed the same topology described previously for the . These results indicate that the DnaJ phylogenetic signal is able to reproduce the accepted relationships among the five classes of the . At a lower taxonomic level, using 20 alphaproteobacteria, the 16S rRNA gene-based phylogeny is distinct from the one based on DnaJ sequence analysis. Although the same clusters are generated, only the topology of the DnaJ tree is consistent with broader phylogenies from recent studies based on concatenated alignments of multiple core genes. For example, the DnaJ tree shows the two clusters within the as closely related, as expected, while the 16S rRNA gene-based phylogeny shows them as distantly related. In order to evaluate the phylogenetic performance of at the genus level, a multilocus analysis based on five housekeeping genes (, , , and ) was performed for ten species. In contrast to the 16S rRNA gene, the DnaJ sequence analysis generated a tree similar to the multilocus dendrogram. For identification of chickpea mesorhizobium isolates, a nucleotide sequence-based tree was used. Despite different topologies, 16S rRNA gene- and -based trees led to the same species identification. This study suggests that the gene is a good phylogenetic marker, particularly for the class , since its phylogeny is consistent with phylogenies based on multilocus approaches.


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vol. , part 12, pp. 2839 - 2849

PCR primers and amplication conditions.

Graphical representation of G+C content (mol%) for alphaproteobacteria.

Phylogeny based on nucleotide sequences of for the genus and chickpea rhizobial isolates.

[PDF file of Supplementary Table and Figures](83 KB)

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