Why prokaryotes have pangenomes

  title={Why prokaryotes have pangenomes},
  author={James O. McInerney and Alan McNally and Mary J. O’Connell},
  journal={Nature Microbiology},
The existence of large amounts of within-species genome content variability is puzzling. Population genetics tells us that fitness effects of new variants—either deleterious, neutral or advantageous—combined with the long-term effective population size of the species determines the likelihood of a new variant being removed, spreading to fixation or remaining polymorphic. Consequently, we expect that selection and drift will reduce genetic variation, which makes large amounts of gene content… 

Selection-based model of prokaryote pangenomes

It is argued that in order to understand the contribution of different mechanisms to pangenome diversity, it is crucial to have empirical information on population structure, gene-by-environment interactions, the distributions of fitness effects and rates of gene gain and loss in different prokaryote groups.

Structure and Dynamics of Bacterial Populations: Pangenome Ecology

There are now numerous examples of relationship between gene variation and niche adaptation, as well as the population genomic footprint left by the dynamics of gene flow, diversification, and adaptation.

Genic Selection Within Prokaryotic Pangenomes

An appreciation for the potential action and implications of genic selection is important to better understand the evolution of prokaryotic pangenomes.

Factors driving effective population size and pan-genome evolution in bacteria

A new model of genome architecture evolution in prokaryotes is pointed to, in which pan-genome sizes, not individual genome sizes, are governed by drift-barrier evolution.

Are pangenomes adaptive or not?

The argument made by McInerney et al. for the general advantageousness of accessory genes mainly rests on the assumption that different strains, sharing few accessory genes, each inhabit distinct, transient niches, and that species with large effective population size have large pangenomes, as these species experience more effective selection.

Pangenomes and Selection: The Public Goods Hypothesis

It is argued that niche adaptation has a major impact on pangenome structure, and the concepts of ‘keystone genes’, whose loss leads to concurrent loss of other genes, and ‘event horizon genes”, whose acquisition may lead to adaptation to novel niches and towards a separate, irreversible evolutionary path are introduced.

The population genetics of pangenomes

Two short papers recently attempted to explain prokaryotic pangenomes in light of population genetic theory, reaching surprisingly different conclusions, which suggest that large populations contain high levels of neutral genetic diversity, and also respond more efficiently to natural selection.

Reply to ‘The population genetics of pangenomes’

An apparent paradox, mammals with small Ne tend to accumulate large genomes because selection against junk DNA is inefficient, however, in prokaryotes it is species with large Ne that tend to have larger genomes and pangenomes.

A non-adaptive demographic mechanism for genome expansion in Streptomyces

It is shown that non-adaptive evolutionary phenomena can explain expansion of microbial genome size, and suggested that this mechanism might explain why so many bacteria with large genomes can be found in soil.



Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations

It is demonstrated that selection for gene loss, and not a shortened genome, per se, drove massive, rapid reduction of accessory genes, indicating that selection can be crucial in eliminating unnecessary genes during the early stages of adaptation to a specialized environment.

Theory of prokaryotic genome evolution

A mathematical model of microbial evolution is developed and tested against extensive data from multiple genome comparisons to indicate that genome evolution is not governed by streamlining but rather, reflects the balance between the benefit of additional genes that diminishes with the genome size and the intrinsic preference for DNA deletion over acquisition.

Migration and horizontal gene transfer divide microbial genomes into multiple niches

An eco-evolutionary model is developed and shows how genetic transfer, even when rare, can transform the evolution and ecology of microbes and explains how ecologically important loci can sweep through competing strains and species.

The Origins of Genome Complexity

It is argued that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size, and provided novel substrates for the secondary evolution of phenotypic complexity by natural selection.

How clonal are bacteria over time?

An analysis of time-course metagenomic data from a lake suggests that a bacterial population’s past clonality (as measured by its genetic diversity) is a good predictor of its futureClonality appears to be relatively – but not completely – stable over evolutionary time.

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

It is shown that paralogs share most protein–protein interactions and genetic regulators, whereas xenologs share very few of them, which suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems.

Slightly Deleterious Mutant Substitutions in Evolution

If this class of mutant substitution is important, it can be predicted that the evolution is rapid in small populations or at the time of speciation5.

Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining.

It is concluded that as the potential energetic benefit gained by deletion of short genomic segments is vanishingly small compared with the deleterious side effects of these deletions, selection for reduced DNA synthesis costs is unlikely to shape the evolution of small genomes.

Trends between gene content and genome size in prokaryotic species with larger genomes.

It is found that large genomes are disproportionately enriched in regulation and secondary metabolism genes and depleted in protein translation, DNA replication, cell division, and nucleotide metabolism genes compared to medium- and small-sized genomes.

Exploring the costs of horizontal gene transfer.

  • D. Baltrus
  • Biology
    Trends in ecology & evolution
  • 2013