Figure 4

SNP distribution profiles. Alignments were performed on a total of 240 sequence segments available for all tested strains of Rhizobium etli. Each nucleotide position in the alignment is represented by a consensus. In instances where half of the strains had the same nucleotide and the other half a different nucleotide, the consensus was defined as the nucleotide present in R. etli CIAT652. Common segments were concatenated according to the gene order found in the CFN42 genome (chromosome and after plasmids), yielding 71,630 aligned base pairs. The numbers of nucleotides differing from the consensus are plotted as bars, across independent windows of 250 nucleotides. The black bars (running downwards) show SNPs present in a single strain; the gray areas indicate when the same SNP pattern was present in at least two strains at the same position within the alignment (patterns A and B); and the white bars indicate polymorphic sites where at least three alleles were present in at least two strains, again within the alignment. Segments showing significant recombination events are indicated by bars at the bottom of the plot, and with bars indicating the genomic location of segments with respect to CFN42 (chromosome, white; plasmids, black).