Contrasting segregation patterns among endogenous retroviruses across the koala population

Abstract

AbstractKoalas (Phascolarctos cinereus) are subject to retroviral infections by the koala retrovirus (KoRV), resulting in accumulation of heritable endogenous KoRV in the koala germline. Like other vertebrates, koalas have experienced a history of retroviral epidemics leaving marks as endogenous retroviruses (ERVs) in their genomes; another recently identified ERV lineage, namedphaCin-β, shows a pattern of recent, possibly current, activity with high insertional polymorphism in the koala population that predates the establishment of endogenous KoRV. We investigate geographic patterns of retrovirus activity, focusing on three distinct ERV lineages of increasing estimated ages from KoRV tophaCin-βand tophaCin-β-like, using a whole-genome sequencing dataset of 430 koalas produced by the Koala Genome Survey. We find thousands of ERV loci across the koala population and identify contrasting patterns of polymorphism. In the youngest established ERV-lineage (KoRV), we identify thousands of integrations among northern individuals. In thephaCin-βERV lineage, which is slightly older yet with overlapping time of activity with KoRV, we observe hundreds of integrations in northern individuals. In southern koalas, however,phaCin-βloci are found at higher frequencies possibly reflecting a bottleneck effect. Overall, the findings suggest high ERV burden in koalas that represent historic retrovirus-host interactions. Importantly, the ERV catalogue supplies improved markers for population conservation genetics of this endangered species.