Investigating the mechanisms of genetic co-option from an endogenous virus through single-cell technologies

The parasitoid wasp Microplitis demolitor shares an intrinsic relationship with an endogenous virus that reproduces within specific cells of the female wasp ovary. This virus assists in the suppression of host immune defenses against wasp offspring during development. Much of the genetic pathway involved in viral replication has been uncovered, but how this process is controlled and initiated within the wasp remains unknown. Here, we performed various methods of single-cell sequencing on the ovaries of M. demolitor to discover the genetic basis behind the initiation of viral replication. Using single-cell RNA-seq, we successfully identified and isolated populations of cells that express markers of viral replication. Within these viral cell populations, bioinformatic tools were used to identify co-expressed gene modules consisting of both viral and non-viral genes to identify putative regulators for the initiation of viral replication. Single-cell ATAC-seq was then used to identify common regions of open chromatin upstream of these gene modules, searching for shared DNA binding motifs. These motifs were then cross referenced with our gene modules to identify genes of interest, specifically transcription factors, as putative regulators for the initiation of viral replication. Our approach has laid the groundwork for further investigation of these putative regulators, not only for M. demolitor, but other closely and distantly related parasitoid wasps that hold similar viral relationships.