A 'pangenome' combines all the genes that can be found in a species. Their structure differs greatly across bacteria; in some species, lots of genes vary between individuals, with ‘accessory’ genes sometimes allowing them to survive antibiotics or act as pathogens. Other species have less fluid (variable) pangenomes, with different individuals having similar genes. However, it’s unclear what drives these differences across species.
Researchers have done a phylogeny-based (evolutionary history) analysis with data from 6221 genomes across 126 species of bacteria. For each species, they used the genomes available to generate their pangenome and calculate how fluid these were.
The results suggested that bacterial lifestyle plays a key role. The researchers consistently found that species which live in more variable environments have more fluid pangenomes, which could reflect adaptive processes, and/or neutral processes. Lead author Dr Anna Dewar said:
“We might be seeing this trend because individuals of species with more variable lifestyles could be under natural selection to gain and lose different kinds of genes as they adapt to different local environments. Additionally, it could be because of neutral processes, such as individuals of species with more variable lifestyles simply encountering a greater diversity of genes, and it may be a combination of the two.”
The researchers also investigated an alternate – though not necessarily mutually exclusive – idea: whether variation in pangenome structure reflects the consequences of different effective population sizes (the number of individuals that contribute to producing a distant future generation). Larger effective population sizes could lead to more open pangenomes through either retaining more neutral genes or allowing more effective selection for different genes in different environments. However, they didn’t see this influence pangenome fluidity. Anna said:
“Species with larger effective population sizes had more fluid genomes, but this appeared to be an artifact of how lifestyle influences both effective population size and pangenome fluidity. Effective population sizes were relatively large in most species that we studied, which is consistent with size neither increasing or limiting variation.”
The researchers hope to expand the dataset in the future to include more species, since currently genome databases are focused on species relevant to humans. They also plan to examine the role of lifestyle in more detail, and how the relative balance of selection vs genetic drift might influence pangenomes.
To read more about this research, published in PNAS, visit: https://www.pnas.org/doi/10.1073/pnas.2320170121
