Comparative Genomics Of Parasitoid Wasps And Parasitism-associated Genomics Features

Parasitoid wasps(order Hymenoptera)are extremely diverse insect with a variety of life history traits,providing an ideal model for studying the speciation,parasitic biology and the mechanism of sex determination in haplodiploidy system.Some parasitoid wasps,for example Nasonia vitripennis,are rapidly emerging as a model for evolutionary and developmental genetics.Furthermore,many parasitoid wasps are natural enemies of most agricultural pests,which makes them very effective for the biological control of pests.Some parasitoid wasps have been used for commercial application of biological control of pests.Therefore,the systematic study of parasitoid wasps is of great significance to both basic research and agricultural production.In this thesis,we firstly generated chromosome-level genome assemblies of two parasitoid wasps(Pteromalus puparum and Cotesia chilonis),then performed comparative genomics analyses to study the parasitism-associated genomics features,including the histone gene evolution,amino acid metabolic pathway evolution as well as host regulation and nutritional(free amino acids)exploitation.(1)Chromosome-level genome assemblies of two parasitoid waspsWe sequenced and assembled high-quality genome assemblies of two parasitoid wasps,P.puparum and C.chilonis using a combination of Illumina short-read,PacBio long-read technologies,which at 338 Mb and 189 Mb,with scaffold N50 of 1.2 Mb and 2.2 Mb,respectively.Based on Hi-C interaction information,we further assembled 738 and 620 scaffolds from P.puparum and C.chilonis draft genomes to chromosome-level genomes,respectively,and obtained 5 chromosomes of P.puparum and 10 chromosomes of C.chilonis.The numbers of assembled chromosomes of these two species are consistent with previous studies on parasitoid karyotype.Assembly assessments revealed that both genome assemblies were highly accurate and near completion,with BUSCO score higher than 96%.In total,we identified 17,656 and 14,142 protein-coding genes in the genomes of P.puparum and C.chilonis,respectively.The chromosome synteny analysis showed a low level of synteny between P.puparum and C.chilonis,suggesting many genome rearrangements have occurred after species divergence.Using the chromosome-level genome assembly,we also investigated the distribution of the venom genes and P450 genes on the chromosomal genome of P.puparum,revealing their evolutionary characteristics.In this study,we constructed high-quality chromosomal genomes of two important parasitoid wasps,and analyzed the chromosomal rearrangement,venom gene evolution and P450 gene evolution.(2)Comparative genomics of HymenopteraWe performed a comparative genomics analysis for 47 hymenopterans,including 4 sawflies(Symphyta),13 ichneumonoid wasps(Ichneumonoidea),1 cynipoid wasp(Cynipoidea),10 chalcid wasps(Chalcidoidea),1 dryinid wasp(Chrysidoidea),3 vespoid wasps(Vespoidea),9 ants and 6 bees(26 of 47 are parasitoid wasps).We generated a phylogenetic tree of these 47 hymenopterans based on 1,495 single copy genes.Estimated divergence times of these hymenopterans were calculated.By comparative genomics analyses,we document the gene gain and loss,gene family expansion and contraction,protein domain family expansion and contraction and protein domain rearrangement during Hymenoptera evolution.We found totally 101 rapid evolving gene families during Hymenoptera evolution.Among them,some gene families are related to environmental perception and detoxification metabolism,such as gustatory receptors,odorant receptors,P450 genes and UGT genes,and we speculated that the rapid evolution of these gene families might be associated with the adaptations to different environments and foods.We also documented some gene families,including cuticular proteins and histones,which only evolved rapidly in parasitoid wasps.Their rapid evolution may be related to parasitic behavior.Our large-scale comparative genomic analysis of Hymenoptera revealed the evolutionary characteristics of the hymenopteran genomes and provided a large number of genetic resources for subsequent studies.(3)Analysis of the histone gene family in parasitoid waspsWe analyzed histone genes of 40 hymenopterans and found that the histone gene family underwent multiple independent expansions in Hymenoptera evolution.Importantly,the expansions of histone genes were significantly enriched in parasitoid wasps.In family Pteromalidae,P.puparum genome showed the most significant histone gene expansion,with 133 histone genes.Synteny analyses of histone genes revealed a poor synteny across Pteromalidae,suggesting the rapid evolution of histone genes.In addition,we found a chalcidoidea-conserved histone H1-like gene.Transcriptomic analysis and qPCR analysis both showed that this histone H1-like gene is specifically highly expressed in male yellow pupae when compared to other developmental stages.Knockdown of this histone H1-like gene in P.puparum significantly increased the proportion of males in the offspring,suggesting this gene may be related to the reproduction of male parasitoid wasps.This study revealed the evolutionary history of the hymenopteran histone gene family and provides a basis for further functional studies.(4)Amino acid synthetic pathways of parasitoid wasps and the host regulation and nutritional exploitationUsing parasitoid wasp C.chilonis and its host Chilo suppressalis as an experimental model,we investigated the amino acid synthetic pathways of parasitoid and host,and the network of parasitoid and host amino acids metabolism by genomic,transcriptomic,and metabolomic data.Genome-wide gene searches showed that both parasitoid wasp and host have lost the synthesis capability of 9 amino acids,valine,leucine,isoleucine,phenylalanine,tryptophan,lysine,histidine,methionine,threonine,due to gene losses in amino acid synthetic pathways.Additionally,C.chilonis further lost the synthesis capability for arginine.Experiments confirm that these 10 amino acids were essential for the development of C.chilonis larvae in vitro.Metabolomic analysis showed that the free amino acids levels in host hemolymph were significantly changed 3 days after parasitism.The contents of arginine,serine,tyrosine and alanine were significantly increased in host hemolymph,while the contents of lysine,methionine and glutamic acid were largely decreased.Additional transcriptomic analyses showed that parasitoids may increase the amino acid content in the host by inhibiting amino acid consumption and promoting protein degradation,which will eventually facilitate larval development.This study provides a new insight into the molecular mechanism of host regulation and free amino acid exploitation by parasitoid wasps and these results can be used to inform the design of parasitoid artificial diets for pest control.