Strong selection and high mutation supply characterize experimental Chlorovirus evolution. Genomic evolution of experimental Chlorovirus evolution

A group of viruses whose evolution has not yet been extensively studied are the Phycodnaviridae, a globally abundant family of freshwater large dsDNA viruses. Here we studied the evolutionary change of this family’s type specimen Paramecium bursaria Chlorella Virus 1 (PBCV-1), during experimental coevolution with its natural host. We used pooled genome sequencing of six independently evolved populations to characterize genomic change over five time points. Across six experimental replicates involving either strong or weak demographic fluctuations, we found single nucleotide polymorphisms (SNPs) at 67 sites. Genomic variation at those sites was highly repeatable, with just two of the SNPs found in only a single experimental replicate. Across the genome, we did not find evidence that non-synonymous SNPs were found in more (or less) replicates than synonymous SNPs, but non-synonymous SNPs did on average reach higher allele frequencies. One SNP was located in an intergenic region, the other 66 were located in twenty open reading frames (ORFs), providing new information about the targets of selection during the Chlorella-Chlorovirus coevolutionary arms race. Three genes showed an excess of variable sites. Allele frequency trajectories over time of the SNPs in these three genes showed that repeated mutations often did not exhibit similar patterns of frequency change in independent evolutionary replicates. In summary, evolution at the molecular level was highly repeatable and the overall amount of genome-wide variation was surprisingly limited, indicating a strong effect of selection.