Fig. 5

Synteny of predicted Protein Encoding Genes and evolutionary relationships among E. aridi strains in relation to PEG orthologies in E. meliloti 1021 replicons. PEG numbers corresponding to the 103 conserved genes among alpha-rhizobial strains and species as well as selected 84 and 55 orthologs from the 6 E. aridi strains (indicated at the right of the top plot) located in scaffolds showing synteny with, respectively pSymA and pSymB of E. meliloti 1021 are represented in (a). The synteny conservation between PEGs corresponding to these three gene sets (b, c and d respectively) were represented by plotting PEG numbers of the LMR001 strains against the other E. aridi strains (indicated on the left side of scatter plots). Evolutionary relationships of the corresponding gene sets upon concatenation (respectively e, f and g) were inferred using Neighbor Joining tree construction as described in Methods; and showed bootstrap values (from 1000 replications in red) near nodes, the scales at the bottom of each tree shows the number of substitutions per site. Strains originating from Morocco, Mexico and India were highlighted respectively in green, purple and blue (showed on the left of the trees). The matrix (h, i and j) show the respective number of variable sites (top right matrix) and percentage identities (bottom left matrix), the color code on the left of the matrix shows the % identity conservation obtained from pair-wise nucleotide sequence comparisons of the 3 concatenated and aligned gene sets obtained for the tree construction of e, f and g respectively. The number of positions aligned for each set is shown on the top left cell in each matrix