A chromosome-scale genome assembly and functional studies implicate the viral RNA polymerase in transcription of most Microplitis demolitor bracovirus late genes

ABSTRACT Microgastroid parasitoids lay eggs in other insects and harbor bracoviruses (BVs), which evolved from a nudivirus. BV genomes are endogenized in the wasp germline and consist of nudivirus-like genes plus proviral segments with virulence genes. Nudivirus genes produce virions in the ovary calyx cells, which wasps use to transfer virulence genes to hosts. Here, we report a chromosome-scale genome assembly for Microplitis demolitor, which harbors Microplitis demolitor bracovirus (MdBV). The assembly identified the locations of all MdBV nudivirus-like genes and proviral segments. Like nudiviruses and related baculoviruses, BVs express nudivirus-like genes in a temporally ordered cascade. Early genes include subunits of an RNA polymerase (RNApol) that transcribes late genes encoding virion components. Promoter motifs in BV relatives did not predict MdBV early and late genes. In contrast, RNA interference experiments showed that knockdown of the MdBV RNApol downregulated most of the known nudivirus-like late genes. We identified 60 genes with no homology with known nudivirus genes, with features indicating that they were also inherited from the BV ancestor. We named these candidate, new nudivirus-like genes. Each was expressed as a late gene, 39 encoded virion components, and orthologs were identified in wasps that are closely related to M. demolitor . Finally, we identified a new 20 bp motif in most MdBV late genes. This motif was present in the nudivirus-like genes of another BV but was largely absent in nudivirus and baculovirus genes. Altogether, the results identified several new features of BVs that are important for virion formation. IMPORTANCE Bracoviruses (BVs) provide a dramatic example of cooption and repurposing of a virus by eukaryotes for new functions. This study further characterizes the gene content and organization of the MdBV genome. Our results support the conclusion that the MdBV RNApol retains conserved functions by primarily transcribing viral late genes. Reported results also present a strategy for identifying BV genes that share no homology with known nudiviruses.