A chromosome scale assembly of the parasitoid wasp Venturia canescens provides insight into the process of virus domestication

Authors: MAO, MENG - University Of Georgia; SIMMONDS, TYLER - Orise Fellow; STOUTHAMER, CORINNE - University Of Georgia; KEHOE, TARA - University Of Georgia; Geib, Scott; BURKE, GAELEN - University Of Georgia

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/31/2023
Publication Date: 6/22/2023
Citation: Mao, M., Simmonds, T., Stouthamer, C., Kehoe, T., Geib, S.M., Burke, G.R. 2023. A chromosome scale assembly of the parasitoid wasp Venturia canescens provides insight into the process of virus domestication. G3, Genes/Genomes/Genetics. Article jkad137. https://doi.org/10.1093/g3journal/jkad137.
DOI: https://doi.org/10.1093/g3journal/jkad137

Interpretive Summary: The parasitoid wasp Venturia canescens is an important biological control agent of moth pests of stored products. This wasp species has an endogenous virus that is associated with it that likely plays an important role in host parasitism success. The goal of this research was to recapitulate the genome of this wasp at a chromosome scale and characterize the viral genes that have become incorporated into the wasp genome. The chromosome scale assembly is organized in 11 chromsomes with a total length of 290 million base pairs. Across these chromosomes, 60 virus derived genes were characterized, in three distinct chromosomes. The genome and characterization of these virus genes provides a foundation for future studies on the evolution and role of virus derived genes in parasitoid wasps.

Technical Abstract: The parasitoid wasp Venturia canescens is an important biological control agent of moth pests of stored products and serves as a model to study the function and evolution of domesticated endogenous viruses (DEVs). The DEVs discovered in V. canescens are known as virus-like particles (VcVLPs), which are produced using nudivirus-derived components and incorporate wasp-derived virulence proteins instead of packaged nucleic acids. Previous studies of virus-derived components in the V. canescens genome identified 53 nudivirus-like genes organized in six gene clusters and several viral pseudogenes, but how VcVLPs have evolved after their integration in the ancestral wasp genome is largely unknown. Here we present a chromosomal scale genome of V. canescens consisting of 11 chromosomes and 56 unplaced small scaffolds. The genome size is 290.8 Mbp with a N50 scaffold size of 24.99 Mbp. A high-quality gene set including 11,831 protein-coding genes were produced using RNA-Seq data as well as publicly available peptide sequences from related Hymenoptera. A manual annotation of genes of viral origin produced 61 intact and 19 pseudogenized nudivirus-derived genes. The genome assembly revealed that previously identified clusters 4 and 5 form a single cluster and the 5 gene clusters comprising of 60 intact nudivirus-derived genes were located in three chromosomes. In contrast, pseudogenes are dispersed among 8 chromosomes with only 4 pseudogenes associated with nudivirus gene clusters. The VcVLP genome architecture suggests it originates from a recent virus acquisition and there is a link between the processes of dispersal and pseudogenization. This high-quality genome assembly and annotation represents the first chromosome-scale assembly for parasitoid wasps associated with VLPs, and is publicly available in the National Center for Biotechnology Information Genome and RefSeq databases, providing a valuable resource for future studies of the VLP evolution in parasitoid wasps.