Is the pan-genome also a pan-selectome?

Abstract

The comparative genomics of prokaryotes has shown the presence of conserved regions containing highly similar genes (the 'core genome') and other regions that vary in gene content (the ‘flexible’ regions). A significant part of the latter is involved in surface structures that are phage recognition targets. Another sizeable part provides for differences in niche exploitation. Metagenomic data indicates that natural populations of prokaryotes are composed of assemblages of clonal lineages or "meta-clones" that share a core of genes but contain a high diversity by varying the flexible component. This meta-clonal diversity is maintained by a collection of phages that equalize the populations by preventing any individual clonal lineage from hoarding common resources. Thus, this polyclonal assemblage and the phages preying upon them constitute natural selection units.

Tales from a thousand and one phages

“…This model can be taken beyond the purely mechanistic level since it implies that the bacterial population actually includes its associated phages as a sort of tax collectors that equate and preserve the efficiency of the system making this consortium of cell clones, plus the phages preying on them, a sort of meta-clonal organism that can be selected upon or extinguished i.e., a unit of selection or selectome. 28 Our results support this view, as the local diversity found at a single marine water column sample is astonishing. Even within relatively similar genomes abundant microdiversity could be established and still some hyperdiversified regions are found identical in genomes isolated from distant locations including the Atlantic and Pacific Oceans.…”

“…27 Airborne transportation in extreme meteorological events might provide faster connection among marine microbial communities that travel in the aerosols formed for example in large storms, but once they arrive to the distant places they would face a huge dilution compared with the local strains. It is possible also that these populations are conserved under the similar conditions of the deep photic zone worldwide because they are selected for 28 (see below).…”

Genomic Diversity of “Deep Ecotype” Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames

“…Basically in all these cases, the fGIs present in different CFs have sets of genes that produce different sugar skeletons that form or decorate the exposed structure. As previously discussed (Rodriguez-Valera et al 2009; Gonzaga et al 2012; Rodriguez-Valera and Ussery 2012), this fGIs could generate different phage recognition targets in the population diluting the predation pressure of these viruses. These fGIs were very well conserved within CFs but were always different for different CFs (table 1).…”

“…The presence of multiple concurrent CFs of A. macleodii has already been explored (Gonzaga et al 2012). Here, we have proven the presence of some of them at different locations, expanding the model (Rodriguez-Valera et al 2009; Rodriguez-Valera and Ussery 2012) and refining the description of the patterns of variation among the different CFs.…”

Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

“…Multiple explanations for the discordance between the high numbers of coexisting closely related genotypes and ecological theory are conceivable. Either (i) the observed genetic variation represents to a large extent neutral diversification (11)(12)(13), (ii) closely related genotypes indeed occupy distinct ecological niches, implicating a vast number of species-like units (14,15), or (iii) concepts of evolution, which were originally developed for macroorganisms, are not readily applicable to microbes, and novel models have to be developed (16)(17)(18)(19).…”