Fig. 2
Comparison of the 16S rRNA gene of Bradyrhizobium elkanii USDA 76T (shown in bold blue print) with those of other proposed Bradyrhizobium species and the serotype strains of the remaining 16 serogroups of the soybean bradyrhizobia. DNA homology affiliation of the different soybean serogroup strains are indicated within the rectangles. DNA homology values for the serogroup strains USDA 4, USDA 94, USDA 124, USDA 126, USDA 127, USDA 129 and USDA 135 were not reported. The sequences were initially aligned by using the software MEGA, version 5 [67]. Subsequently the alignment was manually inspected for errors and necessary corrections were made by using GeneDoc version 2.6.001 [68]. The outgroups Mesorhizobium loti LMG6125T and M. ciceri UPM-Ca7T were chosen because of the reported recombination events between the 16S rRNA genes of B. elkanii and Mesorhizobium [22]. Of the 1313 active sites of the alignment there were 40 gaps among the Bradyrhizobium taxa. The number of different base pairs among all the 35 aligned sequences (including the two Mesorhizobium species) was determined by using MEGA, version 5 [67] to generate a tree using the UPGMA algorithm. Bootstrap analysis [69] with 2000 permutations of the data set was used to determine support for each of the branches. Type strains are indicated by name in the figure. Strains in the figure with a genome sequencing project registered in GOLD [70] are as follows: B. daqingense (2596849087), USDA 110 (640700549), USDA 76 (2513649183), USDA 6 (2513666035), B. pachyrhizi (2655289729), and B. yuanmingense (2617374406)