A chromosome‐level genome assembly of the parasitoid wasp Pteromalus puparum

Abstract

Parasitoid wasps represent a large proportion of hymenopteran species. They have complex evolutionary histories and are important biocontrol agents. To advance parasitoid research, a combination of Illumina short‐read, PacBio long‐read and Hi‐C scaffolding technologies was used to develop a high‐quality chromosome‐level genome assembly for Pteromalus puparum, which is an important pupal endoparasitoid of caterpillar pests. The chromosome‐level assembly has aided in studies of venom and detoxification genes. The assembled genome size is 338 Mb with a contig N50 of 38.7 kb and a scaffold N50 of 1.16 Mb. Hi‐C analysis assembled scaffolds onto five chromosomes and raised the scaffold N50 to 65.8 Mb, with more than 96% of assembled bases located on chromosomes. Gene annotation was assisted by RNA sequencing for the two sexes and four different life stages. Analysis detected 98% of the BUSCO (Benchmarking Universal Single‐Copy Orthologs) gene set, supporting a high‐quality assembly and annotation. In total, 40.1% (135.6 Mb) of the assembly is composed of repetitive sequences, and 14,946 protein‐coding genes were identified. Although venom genes play important roles in parasitoid biology, their spatial distribution on chromosomes was poorly understood. Mapping has revealed venom gene tandem arrays for serine proteases, pancreatic lipase‐related proteins and kynurenine–oxoglutarate transaminases, which have amplified in the P. puparum lineage after divergence from its common ancestor with Nasonia vitripennis. In addition, there is a large expansion of P450 genes in P. puparum. These examples illustrate how chromosome‐level genome assembly can provide a valuable resource for molecular, evolutionary and biocontrol studies of parasitoid wasps.

Chromosome‐level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi‐C technology

“…Additionally, we manually identified venom protein genes of A. gifuensis , as these are one of the most important components for parasitoid wasps to ensure successful parasitism (Asgari & Rivers, 2011). We obtained 41 venom genes through a blast method querying the genome with sequences from several published wasps, such as Apis mellifera (Weinstock et al, 2006), Pteromalus puparum (Ye et al, 2020), Aphidius ervi and Lysiphlebus fabarum (Dennis et al, 2020). Among these genes, 9 venom carboxylesterase‐6, 6 venom serine protease and 5 venom dipeptidyl peptidase showed expansion as identified in CAFÉ analysis (Table S11, Figure S4).…”

“…The expanded venom serine protease may be closely related to the parasitic life history of this wasp, because the protease induces a lethal melanization response and exhibits fibrin(ogen)olytic activity in hosts (Choo et al, 2010). Although the venom proteins have been identified and reported in several parasitoid wasps (Colinet et al, 2013; Danneels et al, 2010; Dennis et al, 2020; Vincent et al, 2010; Ye et al, 2020), the different function of various venom genes still need further study.…”

A high-qualityde novogenome assembly from a single parasitoid wasp

“…In addition, parasitoid wasps are often in very small size, which makes the genome projects of them complicated. Although many studies have assembled genomes from pooled inbred lab strains [8,[22][23][24][25][26][27], most of parasitoid wasps are difficult to be reared in the lab to establish such lab strains for sequencing. There are also some problems and uncertain factors in sequencing field collected samples, such as high heterozygosity and insufficient sample.…”

Effects of sugar sources on adult longevity, survival and related gene expression in an endoparasitoid, Pteromalus puparum (Hymenoptera: Pteromalidae)

“…The colony of P. puparum was continuously cultured in the laboratory for more than ten generations after initially being collected in the field in Hangzhou, China. 29 Pteromalus puparum and its host P. rapae were reared in an artificial climate chamber under the condition of 25 ± 1°C, 60 ± 5% relative humidity and a photoperiod of 16 h:8 h (light/dark). The parasitic wasps were reared in cylindrical polypropylene tubes (24 mm in diameter × 95 mm in length), with no more than 30 individuals in each tube.…”

“…In this study, we tested the effects of two commonly used laboratory sugar sources, honey and sucrose, on the survival of P. puparum female adults and determined the optimal sugar concentrations for wasp lifespan. Subsequently, we analyzed the expression patterns of some selected lifespan‐related genes involved in nutrient sensing pathways, and the correlation between their changes and wasp lifespan, based on a high‐quality chromosome‐level genome assembly 29 and gene annotation of lifespan‐related genes for P. puparum 33 . These findings may reveal the role of these genes in the process of nutrition affected lifespan, and provide a new tool for studying the longevity regulation and aging mechanism of parasitic wasps.…”