While globally, the core gene pools of such bacteria are highly clonal [21], there may be certain plastic regions that experience frequent genomic recasting [22].
Our aim was to further characterize unintrogressed C. coli clades 2 and 3, using comparative genomics and with additional genome sequences available, to investigate the impact of horizontal gene transfer in shaping the accessory and core gene pools in unintrogressed C. coli.
This flexible gene pool of bacteria is composed of prophages and other mobile elements or regions contrary to the core gene pool which comprises of the chromosomal segments pertaining to bacterial metabolic functions [18].
Consequently, genome content can be divided into a core gene pool and a flexible gene pool [ 1- 3].
In fact, the genes constituting a prokaryotic genome appear to be divided into two classes: a "core gene pool" that comprises intrinsic genes encoding the proteins of basic cellular functions, and a "flexible gene pool" that comprises HGT-acquired genes encoding proteins which function under particular conditions, such as genomic islands [ 13].
Next to this apparent habitat specificity, a core chiA gene pool (which was shared across most communities) became visible on the basis of an analysis of occupied band positions.
Comparative analyses of the gene content of the three strains define two distinct gene pools: a core genome, the set of orthologous genes shared by the three strains and a flexible gene pool, the sets of genes that either are common to two species out of three or that do not have any significant homolog in any of the two other species (Figure 1).
Moreover, when we separated essential and nonessential genes into core and attachment proteins, we found that the evolutionary rates of attachment proteins are significantly lower than core proteins in both the gene pools (fig. 2).
Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia.
For example, a recent phylogeographic analysis distinguished two gene pools [ 1]: the vertically inherited core genome and horizontally acquired mobile or mobilizable elements.
Therefore, we could assume that there were at least four distinct clonal lineages at this level of divergence, that is, core genomes at over 98% similarity and very different flexible gene pools.
