Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus

Abstract

Background Biocontrol is a key technology for the control of pest species. Microctonus parasitoid wasps (Hymenoptera: Braconidae) have been released in Aotearoa New Zealand as biocontrol agents, targeting three different pest weevil species. Despite their value as biocontrol agents, no genome assemblies are currently available for these Microctonus wasps, limiting investigations into key biological differences between the different species and strains. Methods and findings Here we present high-quality genomes for Microctonus hyperodae and Microctonus aethiopoides, assembled with short read sequencing and Hi-C scaffolding. These assemblies have total lengths of 106.7 Mb for M. hyperodae and 129.2 Mb for M. aethiopoides, with scaffold N50 values of 9 Mb and 23 Mb respectively. With these assemblies we investigated differences in reproductive mechanisms, and association with viruses between Microctonus wasps. Meiosis-specific genes are conserved in asexual Microctonus, with in-situ hybridisation validating expression of one of these genes in the ovaries of asexual Microctonus aethiopoides. This implies asexual reproduction in these Microctonus wasps involves meiosis, with the potential for sexual reproduction maintained. Investigation of viral gene content revealed candidate genes that may be involved in virus-like particle production in M. aethiopoides, as well as a novel virus infecting M. hyperodae, for which a complete genome was assembled. Conclusion and significance These are the first published genomes for Microctonus wasps which have been deployed as biocontrol agents, in Aotearoa New Zealand. These assemblies will be valuable resources for continued investigation and monitoring of these biocontrol systems. Understanding the biology underpinning Microctonus biocontrol is crucial if we are to maintain its efficacy, or in the case of M. hyperodae to understand what may have influenced the significant decline of biocontrol efficacy. The potential for sexual reproduction in asexual Microctonus is significant given that empirical modelling suggests this asexual reproduction is likely to have contributed to biocontrol decline. Furthermore the identification of a novel virus in M. hyperodae highlights a previously unknown aspect of this biocontrol system, which may contribute to premature mortality of the host pest. These findings have potential to be exploited in future in attempt to increase the effectiveness of M. hyperodae biocontrol.

Immune system modulation & virus transmission during parasitism identified by multi-species transcriptomics of a declining insect biocontrol system

“…Of the total 158 predicted genes in the MhFV genome, 118 are significantly differentially expressed in parasitised ASW (Supplementary Table 4), which could reflect expression within either the oviposited M. hyperodae egg or within ASW tissues themselves. Of these DEGs, 40 had a TPM value above five, and 23 of these also had a Blast or Pfam annotation from a previous analysis [ 35 ]. ORF116 had the highest TPM at 758.95 and is annotated as a lytic polysaccharide mono-oxygenase, which may act to facilitate the spread of the viral infection [ 35 ].…”

“…Of these DEGs, 40 had a TPM value above five, and 23 of these also had a Blast or Pfam annotation from a previous analysis [ 35 ]. ORF116 had the highest TPM at 758.95 and is annotated as a lytic polysaccharide mono-oxygenase, which may act to facilitate the spread of the viral infection [ 35 ]. ORF67 had the second highest TPM for an annotated gene at 87.60 and is annotated as a Jmjc-domain containing protein, involved in transcriptional regulation with a potential eukaryotic origin in LbFV-like viruses [ 35 , 99 ].…”

“…Leptopilina boulardi eggs infected with a related virus, Leptopilina boulardi filamentous virus, are encapsulated significantly less by their Drosophila host [ 16 ], thus MhFV transmission during parasitism could be another factor modulating the ASW immune system during parasitism. MhFV infection has not been detected in any M. aethiopoides strains [ 35 ], and with M. aethiopoides parasitism of ASW also viable [ 134 ], MhFV infection is likely not necessary for successful parasitism of ASW by all Microctonus wasps.…”

“…All RNA-seq samples were quasi-mapped using Salmon v1.5.1 [ 42 ] with default settings, against a concatenated file containing the length-filtered ASW transcriptome, as well as the length-filtered M. hyperodae transcriptome (with any significant hits in the M. hyperodae transcriptome to MhFV genes removed) and predicted genes from the MhFV genome from previous work [ 15 , 35 ]. DESeq2 v1.34 [ 43 ] was used to create the DESeqDataSet (DDS) object, by importing Salmon output files using tximport v1.22 [ 44 ] in R v4.1.3 [ 45 ].…”

“…Here we examine the transcriptional responses of ASW to both parasitism by, and exposure to M. hyperodae , to further understand the interactions between these species, and gain insight into the parasitism decline. By performing a multi-species transcriptomic analysis, we also reveal continued expression of M. hyperodae venom components inside parasitised ASW, as well as transmission of the recently discovered MhFV [ 35 ] to all parasitised ASW and a small number of ASW in which parasitism had not been detected.…”