Overview of genome similarity-based code assignment.

<p>(<b>A</b>) The genome of one organism is chosen as first genome (G1), added to the genome database, and “0” is assigned to all positions in the code (only five positions are shown here for simplicity while codes with 20 positions were used in the examples in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089142#pone-0089142-t002" target="_blank">Tables 2</a> to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089142#pone-0089142-t005" target="_blank">5</a>). A second genome (G2) is then added to the database and compared to G1. A code is assigned to the organism with genome G2 based on the genome similarity to G1 measured as percentage of average nucleotide identity (ANI). (<b>B</b>) The genome of a third organism (G3) is compared to G1 and G2. Since G3 is more similar to G1 than G2, G3 is assigned its code based on its ANI with G1. (<b>C</b>) Every new genome that is added to the database will be compared to all genomes already in the database and codes will always be assigned based on the ANI with the most similar genome. (<b>D</b>) Since every organism in the database was assigned a code based on genome similarity with the most similar organism already in the database at the time of its addition, all codes reflect the similarity of organisms with each other (as long as their genomes aligned) and thus are an approximation of their phylogenetic relationships (represented by the tree in the figure).