Hybrid Genome Assembly and Evidence-Based Annotation of the Egg Parasitoid and Biological Control Agent Trichogramma brassicae

Wolbachia-infected Trichogramma dendrolimi is outcompeted by its uninfected counterpart in superparasitism but does not have developmental delay

BACKGROUND

Wolbachia infection increases the superparasitism frequency of Trichogramma females and provides an opportunity for horizontal intraspecific transmission. However, superparasitism may lead to interstrain competition between Wolbachia-infected Trichogramma offspring and their uninfected counterparts. This study investigated the outcome of interstrain intrinsic competition between Wolbachia-infected thelytokous strain (W) and uninfected bisexual strain (B) of Trichogramma dendrolimi. To determine the developmental rate of both strains, the sizes of immature stages of T. dendrolimi offspring at different times after parasitisation were measured in single parasitism and superparasitism conditions.

RESULTS

The results reflect increased superparasitism by Wolbachia-infected females compared with uninfected females. Trichogramma females did not discriminate between host eggs previously parasitised by either B or W females. When the first oviposition was performed by B females, the B offspring outcompeted W offspring deposited later. Although when W offspring was deposited 8 h earlier than the B offspring, it gained no advantage over B offspring. Regardless of parasitism conditions, differences in the development rate between W and B offspring were not significant.

CONCLUSION

The results reconfirmed that W females presented a higher tendency for superparasitism than B females, and showed that B offspring outcompeted W offspring even when the latter was deposited 8 h earlier. The inferiority of Wolbachia-infected Trichogramma compared with their uninfected counterparts is not due to the developmental delay. This study provides insights into the effects of intrinsic competition on the control efficacy of Wolbachia-infected Trichogramma against pests in biological control programs. © 2022 Society of Chemical Industry.

Genetic relationships among laboratory lines of the egg parasitoid Trissolcus japonicus from native and adventive populations

Candidate biological control agents of invasive insect pests are increasingly being found in new geographic regions as a result of unintentional introductions. However, testing the degree of genetic differentiation among adventive and native-range populations of these agents is rarely done. We used reduced-representation sequencing of genomic DNA to investigate the relationships among laboratory lines of Trissolcus japonicus (Ashmead) (Hymenoptera, Scelionidae), an egg parasitoid and biological control agent of the brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera, Pentatomidae). We compared sequences from multiple adventive populations in North America (Canada, USA) and Europe (Switzerland) with populations sourced from part of its native range in China. We found considerably more genetic variation among lines sourced from adventive populations than among those within native populations. In the Pacific Northwest of North America (British Columbia, Canada and Washington State, USA), we found preliminary evidence of three distinct genetic clusters, two of which were highly dissimilar from all other lines we genotyped. In contrast, we found that other adventive lines with close geographic proximity (two from Ontario, Canada, three from Switzerland) had limited genetic variation. These findings provide a basis for testing biological differences among lines that will inform their use as biological control agents, and provide evidence to support a hypothesis of several independent introductions of T. japonicus in western North America from different source areas.

Genome Assembly and Comparative Analysis of the Egg Parasitoid Wasp Trichogramma dendrolimi Shed Light on the Composition and Evolution of Olfactory Receptors and Venoms

Trichogramma dendrolimi is one of the most successfully industrialized Trichogramma species used to control agricultural and forestry pests in China. However, the molecular mechanisms underlying its host recognition and parasitism remain largely unknown, partially due to the limited genome information of this parasitoid wasp. Here, we present a high-quality de novo assembly of T. dendrolimi through a combination of Illumina and PacBio sequencing technologies. The final assembly had a length of 215.2 Mb and contains 316 scaffolds with a scaffold N50 size of 1.41 Mb. Repetitive sequences with a length of 63.4 Mb and 12,785 protein-coding genes were identified. Significantly expanded gene families were identified to be involved in the development and regulatory processes, while remarkably contracted gene families were involved in the transport processes in T. dendrolimi. The olfactory and venom-associated genes were identified in T. dendrolimi and 24 other hymenopteran species, using uniform methods combining BLAST and HMM profiling. The identified venom genes of T. dendrolimi were enriched in antioxidant activity, tricarboxylic acid cycle, response to oxidative stress and cell redox homeostasis. Our study provides an important resource for comparative genomics and functional studies to interpret the molecular mechanisms underlying host recognition and parasitism of Trichogramma species.

Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea

Crops genetically engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis have advanced pest management, but their benefits are diminished when pests evolve resistance. Elucidating the genetic basis of pest resistance to Bacillus thuringiensis toxins can improve resistance monitoring, resistance management, and the design of new insecticides. Here, we investigated the genetic basis of resistance to Bacillus thuringiensis toxin Cry1Ac in the lepidopteran Helicoverpa zea, one of the most damaging crop pests in the United States. To facilitate this research, we built the first chromosome-level genome assembly for this species, which has 31 chromosomes containing 375 Mb and 15,482 predicted proteins. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250-kb quantitative trait locus on chromosome 13 that was strongly associated with resistance in a strain of Helicoverpa zea that had been selected for resistance in the field and lab. The mutation in this quantitative trait locus contributed to but was not sufficient for resistance, which implies alleles in more than one gene contributed to resistance. This quantitative trait locus contains no genes with a previously reported role in resistance or susceptibility to Bacillus thuringiensis toxins. However, in resistant insects, this quantitative trait locus has a premature stop codon in a kinesin gene, which is a primary candidate as a mutation contributing to resistance. We found no changes in gene sequence or expression consistently associated with resistance for 11 genes previously implicated in lepidopteran resistance to Cry1Ac. Thus, the results reveal a novel and polygenic basis of resistance.

Comparative Genomics Sheds Light on the Convergent Evolution of Miniaturized Wasps

Miniaturization has occurred in many animal lineages, including insects and vertebrates, as a widespread trend during animal evolution. Among Hymenoptera, miniaturization has taken place in some parasitoid wasp lineages independently, and may have contributed to the diversity of species. However, the genomic basis of miniaturization is little understood. Diverged approximately 200 Ma, Telenomus wasps (Platygastroidea) and Trichogramma wasps (Chalcidoidea) have both evolved to a highly reduced body size independently, representing a paradigmatic example of convergent evolution. Here, we report a high-quality chromosomal genome of Telenomus remus, a promising candidate for controlling Spodoptera frugiperda, a notorious pest that has recently caused severe crop damage. The T. remus genome (129 Mb) is characterized by a low density of repetitive sequence and a reduction of intron length, resulting in the shrinkage of genome size. We show that hundreds of genes evolved faster in two miniaturized parasitoids Trichogramma pretiosum and T. remus. Among them, 38 genes exhibit extremely accelerated evolutionary rates in these miniaturized wasps, possessing diverse functions in eye and wing development as well as cell size control. These genes also highlight potential roles in body size regulation. In sum, our analyses uncover a set of genes with accelerated evolutionary rates in Tri. pretiosum and T. remus, which might be responsible for their convergent adaptations to miniaturization, and thus expand our understanding on the evolutionary basis of miniaturization. Additionally, the genome of T. remus represents the first genome resource of superfamily Platygastroidea, and will facilitate future studies of Hymenoptera evolution and pest control.

Genome assemblies of three closely related leaf beetle species (Galerucella spp.)

Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here, we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla, and G. tenella. The three assemblies have a genome size ranging from 460 to 588 Mbp, with N50 from 31,588 to 79,674 kbp, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.

Molecular Characterization of Donacia provosti (Coleoptera: Chrysomelidae) Larval Transcriptome by De Novo Assembly to Discover Genes Associated with Underwater Environmental Adaptations

Simple Summary

Donacia provosti is one of the major pests of aquatic crops. It has been widely distributed in the world causing extensive damage to lotus and rice plants. The larvae generally live-in water; however, little is known about the evolution and molecular mechanisms underlying the adaptation. Here, we generated the first larval transcriptome of D. provosti in order to identify potential genetic mechanisms of aquatic adaptation. About 5036 orthologous clusters were identified among four species and 494 unique clusters were identified from D. provosti larvae including the visual perception. Moreover, 93 orthologous gene pairs were found evolving under positive selection. Our results also showed that 4 gene pairs out of the 93 gene pairs were associated with the “mTOR signaling pathway”, which are predicted to be involved in the molecular mechanism of D. provosti adaptation to the underwater environment. In the light of the increasing availability of transcriptomic information for beetle underwater habitat and evolutionary analyses, it is expected that this paper will provide us with some novel insights into aquatic adaptation in beetles and serves as a foundation for future studies aiming to identify candidate genes underlying the genetic basis of aquatic adaptation in beetles.

Abstract

Donacia provosti (Fairmaire, 1885) is a major pest of aquatic crops. It has been widely distributed in the world causing extensive damage to lotus and rice plants. Changes in gene regulation may play an important role in adaptive evolution, particularly during adaptation to feeding and living habits. However, little is known about the evolution and molecular mechanisms underlying the adaptation of D. provosti to its lifestyle and living habits. To address this question, we generated the first larval transcriptome of D. provosti. A total of 20,692 unigenes were annotated from the seven public databases and around 18,536 protein-coding genes have been predicted from the analysis of D. provosti transcriptome. About 5036 orthologous cutlers were identified among four species and 494 unique clusters were identified from D. provosti larvae including the visual perception. Furthermore, to reveal the molecular difference between D. provosti and the Colorado potato beetle Leptinotarsa decemlineata, a comparison between CDS of the two beetles was conducted and 6627 orthologous gene pairs were identified. Based on the ratio of nonsynonymous and synonymous substitutions, 93 orthologous gene pairs were found evolving under positive selection. Interestingly, our results also show that there are 4 orthologous gene pairs of the 93 gene pairs were associated with the “mTOR signaling pathway”, which are predicted to be involved in the molecular mechanism of D. provosti adaptation to the underwater environment. This study will provide us with an important scientific basis for building effective prevention and control system of the aquatic leaf beetle Donacia provosti.

Next-generation biological control: the need for integrating genetics and genomics

Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.