Functional profiling and evolutionary analysis of a marine microalgal virus pangenome

Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host–virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic interpretation of these viruses is hampered by a lack of functional information, stemming from the surprising number of hypothetical genes of unknown function. It is also unclear how many of these genes are widely shared within the clade. Using one of the most extensively characterized genera, Coccolithovirus, as a case study, we combined pangenome analysis, multiple functional annotation tools, AlphaFold structural modeling, and literature analysis to compare the core and accessory pangenome and assess support for novel functional predictions. We determined that the Coccolithovirus pangenome shares 30% of its genes with all 14 strains, making up the core. Notably, 34% of its genes were found in at most three strains. Core genes were enriched in early e..., AlphaFold v2.1.1 run on each EhV-86 protein (several were too large and not included here) using the full set of databases as outlined by the tool., Any text-editor and protein structure visualization software (e.g. PyMOL).