Unique core genomes of a group of isolates. (A) Shown is the pan-genome of four genomes A, B, C and D (dashed lines) from different taxa with its core-genome (black area), unique genes of each genome (white areas) and the accessory genome (hatched and dotted areas). The accessory genome is composed of unique core genomes, i.e. the intersections of the gene content of all combinations of sub-groups of genomes. The number of possible combinations for n genomes is (including the core-genome and the set of unique genes of each genome). Hence, the maximum number of genome combinations of sub-groups that can form a unique core genome is . In case of a maximum of 10 different unique core genomes can be formed as the intersection of either two (hatched areas) or three different genomes (dotted areas). The size of each unique core genome is given by the number of homolog clusters shared by the particular group of isolates. (B) Unique core genes are found either in isolates of phylogenetically coherent, i.e., monophyletic groups or in groups of isolates that did not derive from a closest common ancestor (genophyletic).
Kahlke et al. BMC Genomics 2012 13:179 doi:10.1186/1471-2164-13-179