The Presence of Ancient Core Genes Reveals Endogenization from Diverse Viral Ancestors in Parasitoid Wasps

Abstract

The Ichneumonoidea (Ichneumonidae and Braconidae) is an incredibly diverse superfamily of parasitoid wasps that includes species that produce virus-like entities in their reproductive tracts to promote successful parasitism of host insects. Research on these entities has traditionally focused upon two viral genera Bracovirus (in Braconidae) and Ichnovirus (in Ichneumonidae). These viruses are produced using genes known collectively as endogenous viral elements (EVEs) that represent historical, now heritable viral integration events in wasp genomes. Here, new genome sequence assemblies for 11 species and 6 publicly available genomes from the Ichneumonoidea were screened with the goal of identifying novel EVEs and characterizing the breadth of species in lineages with known EVEs. Exhaustive similarity searches combined with the identification of ancient core genes revealed sequences from both known and novel EVEs. One species harbored a novel, independently derived EVE related to a divergent large double-stranded DNA (dsDNA) virus that manipulates behavior in other hymenopteran species. Although bracovirus or ichnovirus EVEs were identified as expected in three species, the absence of ichnoviruses in several species suggests that they are independently derived and present in two younger, less widespread lineages than previously thought. Overall, this study presents a novel bioinformatic approach for EVE discovery in genomes and shows that three divergent virus families (nudiviruses, the ancestors of ichnoviruses, and Leptopilina boulardi Filamentous Virus-like viruses) are recurrently acquired as EVEs in parasitoid wasps. Virus acquisition in the parasitoid wasps is a common process that has occurred in many more than two lineages from a diverse range of arthropod-infecting dsDNA viruses.

Keywords: Ichneumonoidea; endogenous virus element (EVE); parasitoid wasp genomes; polydnaviruses (PDVs); virus.

Fig. 1.

Maximum likelihood tree of Ichneumonoidea from Sharanowski et al. (2021). Subfamilies with multiple representatives (except the microgastroid complex, Campopleginae, and Banchinae) have been collapsed for viewing subfamily relationships, the presence and distribution of EVEs, and representative species analyzed in this study. Subfamilies with previously published, genetically characterized EVEs are shaded in boxes, and to the right, independent origins of EVEs, the type of virus ancestor they are derived from, and their known or assumed distribution is indicated. Two nodes within the Campopleginae are highlighted showing that the subfamily is divided into two major clades. Species analyzed in this study are placed next to the subfamily to which they belong and are colored blue (new genome assemblies) and brown (previously published genome assemblies). Taxa marked with an asterisk after the name have uncertain species identification. Support for the tree is robust and can be viewed in detail in Sharanowski et al. (2021).

Fig. 2.

Genes of viral origin in wasp genomes are related to genes in large dsDNA viruses. Maximum likelihood phylogenies constructed from protein sequences of individual genes are shown, with numbers on nodes indicating support from 100 bootstrap replicates. Colored branches indicate virus families or groups. The sequences used for alignment were obtained from Microplitis demoltior bracovirus (MdBV), Cotesia congregata bracovirus (CcBV), Chelonus insularis bracovirus (CiBV), a C. chilonis transcriptome, Eurytoma brunniventris endogenous nudivirus alpha (EbENV-a), Eurytoma brunniventris endogenous nudivirus beta (EbENV-b), Tipula oleracea nudivirus (ToNV), Heliothis zea nudivirus 2 (HzNV-2), Penaeus monodon nudivirus (PmNV), Venturia canescens endogenous nudivirus (VcENV), Drosophila innubila nudivirus (DiNV), Oryctes rhinoceros nudivirus (OrNV), Fopius arisanus endogenous nudivirus (FaENV), Gryllus bimaculatus nudivirus (GbNV), Autographa californica multiple nucleopolyhedrovirus (AcMNPV), Cydia pomonella granulovirus (CpGV), Neodiprion sertifer nucleopolyhedrovirus (NeseMNPV), Culex nigripalpus nucleopolyhedrosis virus (CuniNPV), Glossina pallidipes salivary gland hytrosavirus (GpSGHV), and Musca domestica salivary gland hytrosavirus (MdSGHV), L. boulardi filamentous virus (LbFV), L. boulardi endogenous filamentous virus (LbEFV), Leptopilina heterotoma endogenous filamentous virus (LhEFV), Leptopilina clavipes endogenous filamentous virus (LcEFV), A. mellifera filamentous virus (AmFV), White spot syndrome virus (WSSV), Chionoecetes opilio bacilliform virus (CoBV), Amsacta moorei entomopoxvirus (AMEV), Melanoplus sanguinipes entomopoxvirus (MSEV), Vaccinia virus (VACV), Invertebrate iridescent virus 6 (IIV-6), LDV1, Trichoplusia ni ascovirus 3e (TnAV-3e), Paramecium bursaria chlorella virus 1 (PbCV1), Acanthamoeba polyphaga mimivirus (ApMV), Human herpesvirus 3 (HHV-3), supplementary table S5, Supplementary Material online. Sequences from the IVSPERs of the ichnovirus in Glypta fumiferanae and nimavirus p33 homologs were not included because they were too divergent compared with the other included sequences. Scale bars indicate substitutions per amino acid residue. For ORFs found in wasp genomes, the accession number or scaffold name is followed by an underscore and the ORF number.

Fig. 3.

IVSPER genes identified in the Lissonota genome and synteny with Glypta fumiferanae. Glypta fumiferanae sequences are shown above with Lissonota sequences shown below. Homologous genes with synteny between the two species are indicated by gray shading. Some genes are present in banchine and campoplegine species (G. fumiferanae, Lissonota, and Hyposoter didymator; colored orange) whereas others are present only in the two banchine species presented here (blue). Genes colored beige are homologous to other IVSPER genes but are not detected in syntenous regions of the G. fumiferanae genome.

Fig. 4.

Regions of the Dolichomitus genome similar to the L. boulardi Filamentous Virus (LbFV). Homologous genes with synteny between contigs are indicated by gray shading. Genes with homology to LbFV are highlighted red, genes with homology to LbFV-like genes in Cotesia vestalis are shaded yellow, and other predicted genes are colored white. FVU = Filamentous Virus Unknown protein encoding gene. ORFs shown in deep purple represent pieces of pseudogenes that can be found intact on other contigs. Three short nodes with incomplete gene sequences were not included in this figure (NODE_51377 and NODE_267127 containing pif-0, and NODE_236835 containing lef-9).

Fig. 5.

Regions of the Cotesia vestalis Andong genome similar to the LbFV. Genes with homology to LbFV are highlighted red, pseudogenes as a deep purple. Genes with homology to LbFV-like genes in Dolichomitus are shaded yellow or purple if pseudogenized (FVU = Filamentous Virus Unknown protein encoding gene). Other predicted genes are shaded in gray. Genes with blue background shading have eukaryotic structure (introns and exons), and of these, genes with dark blue colored exons are “high confidence” given evidence from EST alignments.

Fig. 6.

Phylogenetic analysis of arthropod-infecting large dsDNA viruses and parasitoid EVEs. Relationships were derived using a maximum likelihood analysis from 12 core genes with a total of 5003 characters from concatenated amino acid sequences. Bootstrap values over 50% are indicated near the relevant node. Scale bar indicates average number of amino acid substitutions per site. Names of EVEs are highlighted with bold type. Taxa are named as in figure 1, with the addition of Phanerotoma bracovirus (PhBV), Cotesia vestalis bracovirus (CvBV), DoEFV, and CvFV/CvEFV. EbrENV-a was omitted because only one sequence (DNA polymerase) was available.