Rates of Synonymous Substitutions

We used the rate of neutral substitutions at the third codon position as a measure of the rate of divergence between pairs of genes. To do this, we first identified homologous proteins, by using the same BDBH criteria described above, in the chromosomes and symbiotic plasmids of selected Rhizobium genome pairs shown in Figure 7. These homologous proteins were retro-translated into the corresponding codons in the nucleotide sequence; then, the rate of synonymous substitutions at the third codon position was determined with the Ka/Ks calculator (Zhang et al., 2013).

Phylogenetic tree of NodC from the Rhizobium plasmids. NodC proteins from 45 complete Rhizobium genomes were first identified by BLASTp. Phylogenies were estimated with the maximum likelihood method with the JTT matrix and a bootstrap of n = 1000 replicates (see section “Materials and Methods”). In red color, strains with completely sequenced pSyms are indicated.