Additional file 1: Figure S1. of Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

The number of genomes in which each marker gene is identified. Out of the 79 potential marker genes, 73 are present in at least 90 % of the genomes. Figure S2. Spearman’s correlation between each marker gene and the average AAI for all complete genomes. Genes are ordered in the same way as in Fig. 3. Figure S3. Trees generated based on AAI and on percent identities of each marker gene (including 16s rRNA), for the Escherichia/Shigella clade. Figure S4. Trees generated based on AAI and on percent identities of each marker gene (including 16s rRNA), for the Streptococcus clade. Figure S5. Trees generated based on AAI and on percent identities of each marker gene (including 16s rRNA), for the Bacillus clade. Table S1. List of 79 potential marker genes surveyed, out of which 73 were found to be present in at least 90 % of the genomes. Table S2. Alternative names of 79 potential marker genes surveyed. Table S3. Split distances between UPGMA tree generated using AAI and that generated using the percent identities of each marker gene, shown in correspondence with the average percent identity ranks of the marker genes. Table S4. Designed primers for each of the 10 genes that were least conserved in their sequences in the Escherichia/Shigella lineage. (ZIP 3355 kb)