PCR-RFLP with nine restriction enzymes was applied to the 16S and 23S rRNA genes of 42 rhizobial and agrobacterial strains to determine the phylogenetic position of and increase the understanding of the evolution of ribosomal operons. The strains were selected based on previous phylogenetic studies. PCR primers were designed so that they amplified a 2·3 kb fragment of the 23S rRNA gene (excluding the B8 loop). Universal primers rD1 and fD1 were used to amplify the full-length 16S rRNA. The RFLP analysis resulted in 27 and 32 different restriction patterns for 16S and 23S, respectively. The RFLP patterns were transformed to genetic distances and dendrograms were constructed from the data using the unweighted pair group method with averages. The shapes of the dendrograms derived from the analysis of the 16S and 23S rRNA genes correlated well, with only a few strains having different positions. The 23S tree generally had deeper branching than the 16S tree, allowing better discrimination between species and strains. The combined data from the two analyses described 36 genotypes. The eight strains formed a homogeneous cluster in all dendrograms. The RFLP analysis was confirmed by partial sequence analysis of the 16S rRNA gene (the first 800 bp), which correlated well with full-length 16S rRNA sequence analysis. The 16S data placed near the genus with as its nearest neighbour, whereas in the 23S and the combined dendrograms it showed closer affinity to the genus .


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