Evidence of Selection upon Genomic GC-Content in Bacteria

TLDR

Bacterial genomic GC‑content ranges from less than 20 % to over 70 % and is generally attributed to differences in mutational patterns. The study tests the hypothesis that mutation bias explains GC‑content variation by analyzing synonymous polymorphism across 149 bacterial species. The authors analyze synonymous polymorphism data from 149 bacterial species to test this hypothesis. The analysis reveals a widespread excess of GC→AT synonymous mutations inconsistent with mutation bias, translational selection, or biased gene conversion, indicating positive selection for higher GC‑content that extends to overall genomic base composition in many bacteria.

Abstract

The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.