Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes

Abstract

Cytomegalovirus is a genus of herpesviruses, members of which share a long history of co-evolution with their primate hosts including Great Apes, Old and New World monkeys. These viruses are ubiquitous within their host populations and establish lifelong infection in most individuals. Although asymptomatic in healthy individuals, infection poses a significant risk to individuals with a weakened or underdeveloped immune system. The genome of human cytomegalovirus is the largest among human-infecting viruses, and comprises at least fifteen separate gene families, which may have arisen by gene duplication. Within human cytomegalovirus, the RL11 gene family is the largest. RL11 genes are non-essential in vitro but have immune evasion roles that are likely critical to persistence in vivo. These genes demonstrate an extreme level of inter-species and intra-strain sequence diversity, that makes it challenging to deduce the evolutionary relationships within this gene family. Understanding the evolutionary relationships of these genes, especially accurate ortholog identification, is essential for reconstructing ancestral genomes, deciphering gene repertoire and order, and enabling reliable functional analyses across the Cytomegalovirus species, thereby offering insights into evolutionary processes, genetic diversity, and the functional significance of genes. In this work, we combined in silico genome screening with sequence-based and structure-guided phylogenetic analysis to reconstruct the evolutionary history of the RL11 gene family. We confirmed that RL11 genes are unique to cytomegaloviruses of Old World monkeys and Great Apes, showing that this gene family was formed by multiple early duplication events and later lineage-specific losses. We identified four main clades of RL11 genes and showed that their expansions were mainly lineage-specific and happened independently in cytomegaloviruses of Great Apes, African Old World monkeys and Asian Old World monkeys. We also identified groups of orthologous genes across the Cytomegalovirus tree showing that some human cytomegalovirus-specific RL11 genes emerged before the divergence of human and chimpanzee cytomegaloviruses but were subsequently lost in the latter. The extensive and dynamic species-specific evolution of this gene family suggests their functions target elements of host immunity that have similarly co-evolved during speciation.