Drivers of genome segment frequency variation in multipartite viruses in natural plant ecosystems.

Multipartite viruses package their genome segments into separate particles, all of which are required to initiate infection in the host cell. This genome organization is considered costly, and the benefit of multipartite genome organization is not well understood. One hypothesized benefit of multipartition is that it allows for flexible changes in gene expression by altering the frequency of each genome segment, depending on the host or environment. The frequencies of all segments are referred to as the genome formula. In this thesis, I will explore (genetic) variation in natural multipartite virus populations to understand how ecological factors affect their prevalence and genome formula. In the first WP, I will develop a new method for measuring the genome formula using an innovative Nanopore sequencing based approach, and compare this method to other more conventional methods such as qPCR. In the second WP, the genome formula of cucumber mosaic virus (CMV) in mixed infection with alfalfa mosaic virus and potato virus Y is measured to determine whether mixed infection affects accumulation. In the third WP, I determine the prevalence, diversity, and variation of (multipartite) viruses in Dutch ecosystems by sequencing whole plant viromes for eight plant species across early, mid, and late stages of succession in a chronosequence representative of land-use change.