High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus

Evaluation of candidate reference genes for gene expression research in Vespula vulgaris

Introduction

Vespula vulgaris is an invasive wasp that causes considerable detriment to native birds and invertebrates in New Zealand. Reducing at least 80% of invasive wasp densities is necessary to manage the problems this species presents to its invaded range. To explore the function of target genes for the genetic management of V. vulgaris, screening of appropriate reference genes is crucial for conducting the reverse transcriptase-quantitative real-time PCR (RT-qPCR). The selection of appropriate reference genes is an important but often overlooked consideration when delving into RNA research. Many studies rely on one of two tried and trusted reference genes widely used in the literature, which may not be suitable for the normalization of data under particular variables.

Methods

Here, I selected six reference genes of V. vulgaris and evaluated their stability across two conditions: developmental stage and sex by using five different tools for analysis: the ΔCt method, geNorm, NormFinder, BestKeeper, and RefFinder.

Results

Differing appropriate reference genes for different research foci: TBP, EF1A, RPL18X3, and CAPZB for developmental stage treatment, and KTB, EF1A, and CAPZB amongst the sexes.

Discussion

My study further emphasizes that there is no "one size fits all" reference gene, and advocates for analysis of reference gene suitability when conducting gene quantification experiments.

Tolerance and efficient metabolization of extremely high ethanol concentrations by a social wasp

Ethanol, a natural by-product of sugar fermentation, can be found in various fruits and nectar. Although many animals routinely consume ethanol in low concentrations as part of their natural diets, its inherent toxicity can cause severe damage. Even species particularly well adapted to ethanol consumption face detrimental effects when exposed to concentrations above 4%. Here, we investigated the metabolism of ethanol and its impact on survival and behavior in the Oriental hornet (Vespa orientalis), a social wasp that naturally consumes ethanol. We show that chronic ethanol consumption, even at concentrations as high as 80%, had no impact on hornet mortality, construction behavior, or agonistic behavior. Using 13C1 labeled ethanol, we show that hornets efficiently metabolized ingested ethanol and at a much higher rate than honey bees. The presence of multiple copies of the alcohol dehydrogenase (NADP+) gene in the Vespa genera suggests a potential mechanism for ethanol tolerance. These findings support the hypothesis that the mutualistic relationship between ethanol-producing organisms and vespid hosts may be at the origin of their remarkable capacity to utilize and metabolize ethanol.

The tracheal system of the Common Wasp (Vespula vulgaris) - A micro-CT study

X-ray micro-CT has been used to study the tracheal system of Pre and Post hibernation Queen wasps (Vespula vulgaris) and their workers. We have compared our findings in wasps with Snodgrass's description of the tracheal system of the honeybee as characterised by anatomical dissection. Our images, whilst broadly similar, identify the tracheal system as being considerably more complex than previously suggested. One of the 30 wasps imaged had a markedly different, previously undescribed tracheal system. Since completing this study, a large micro-CT study from the American Museum of Natural History (AMNH) has been published. This used different software (Slicer) and analysed 16bit digital data. We have compared our methods with that described in the AMNH publication, adopted their suggested nomenclature and have made recommendations for future studies.

Galba: genome annotation with miniprot and AUGUSTUS

BACKGROUND

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes.

RESULTS

Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments.

CONCLUSIONS

Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.

Current stewardship practices in invasion biology limit the value and secondary use of genomic data

Invasive species threaten native biota, putting fragile ecosystems at risk and having a large-scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole-genome sequences lies an opportunity for cross-species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole-genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field-collected samples. Seventy-six assemblies (38%) reported an 'undescribed' sample origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field-collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% (n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large-scale consortia tended to provide the most complete metadata submissions in our analysis-such cross-institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.

Honey bees and social wasps reach convergent architectural solutions to nest-building problems

The hexagonal cells built by honey bees and social wasps are an example of adaptive architecture; hexagons minimize material use, while maximizing storage space and structural stability. Hexagon building evolved independently in the bees and wasps, but in some species of both groups, the hexagonal cells are size dimorphic-small worker cells and large reproductive cells-which forces the builders to join differently sized hexagons together. This inherent tiling problem creates a unique opportunity to investigate how similar architectural challenges are solved across independent evolutionary origins. We investigated how 5 honey bee and 5 wasp species solved this problem by extracting per-cell metrics from 22,745 cells. Here, we show that all species used the same building techniques: intermediate-sized cells and pairs of non-hexagonal cells, which increase in frequency with increasing size dimorphism. We then derive a simple geometric model that explains and predicts the observed pairing of non-hexagonal cells and their rate of occurrence. Our results show that despite different building materials, comb configurations, and 179 million years of independent evolution, honey bees and social wasps have converged on the same solutions for the same architectural problems, thereby revealing fundamental building properties and evolutionary convergence in construction behavior.

GALBA: Genome Annotation with Miniprot and AUGUSTUS

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein- to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a previously unannotated land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.

A perspective on the expansion of the genetic technologies to support the control of neglected vector-borne diseases and conservation

Genetic-based technologies are emerging as promising tools to support vector population control. Vectors of human malaria and dengue have been the main focus of these development efforts, but in recent years these technologies have become more flexible and adaptable and may therefore have more wide-ranging applications. Culex quinquefasciatus, for example, is the primary vector of avian malaria in Hawaii and other tropical islands. Avian malaria has led to the extinction of numerous native bird species and many native bird species continue to be threatened as climate change is expanding the range of this mosquito. Genetic-based technologies would be ideal to support avian malaria control as they would offer alternatives to interventions that are difficult to implement in natural areas, such as larval source reduction, and limit the need for chemical insecticides, which can harm beneficial species in these natural areas. This mosquito is also an important vector of human diseases, such as West Nile and Saint Louis encephalitis viruses, so genetic-based control efforts for this species could also have a direct impact on human health. This commentary will discuss the current state of development and future needs for genetic-based technologies in lesser studied, but important disease vectors, such as C. quinquefasciatus, and make comparisons to technologies available in more studied vectors. While most current genetic control focuses on human disease, we will address the impact that these technologies could have on both disease and conservation focused vector control efforts and what is needed to prepare these technologies for evaluation in the field. The versatility of genetic-based technologies may result in the development of many important tools to control a variety of vectors that impact human, animal, and ecosystem health.

Early queen joining and long-term queen associations in polygyne colonies of an invasive wasp revealed by longitudinal genetic analysis

Invasive social insects rank among the most damaging of terrestrial species. They are responsible for extensive damage and severely threaten the biodiversity of environments where they are introduced. Variation in colony social form commonly occurs in introduced populations of yellowjacket wasps (genus Vespula). In particular, invasive colonies may contain multiple queens (i.e., polygyne) and persist several years, while in the native range, the colonies are usually annual and harbor a single queen (i.e., monogyne). In this study, we used genome-wide loci obtained by double digest restriction site-associated DNA sequencing (RADseq) to investigate the genetic structure and queen turnover in colonies of the western yellowjacket, Vespula pensylvanica, in their introduced range in Hawaii. Of the 27 colonies monitored over four months (October-January), 19 were polygyne and already contained multiple queens on the first day of sampling. Contrary to previous speculation, this finding suggests that polygyny often arises early in the annual colony cycle, before the production of new queens in the fall. Furthermore, polygyne colonies exhibited a prolonged average lifespan relative to those headed by a single queen. As a result, there is no clear window during which colony eradication efforts would be more effective than upon first discovery. The relatedness among nestmate queens was slightly above zero, indicating that these colonies are generally composed of nonrelatives. The queen turnover within each colony was low, and we detected some full-sibling workers sampled up to four months apart. Finally, we did not detect any population structure among colonies, suggesting that queens disperse up to several kilometers. Taken together, our results provide the first insights into the requeening dynamics in this invasive and incipiently polygyne population and illuminate the early establishment of multiple long-lasting queens in these damaging colonies.

Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

Gene drive and RNAi technologies: a bio-cultural review of next-generation tools for pest wasp management in New Zealand

There is a global need for novel, next-generation technologies and techniques to manage pest species. We review work on potential step-changing technologies for large landscape (>1000 hectares) pest management of social Vespula wasps. We also review Māori perspectives on these controls to gauge social and cultural acceptability to research, test and use of novel controls. Approaches discussed are the use of gene silencing (RNAi) and gene drives (CRISPR-Cas 9) involving genetic modification, which has potential for pest control but vary in feasibility, cost, benefits and off-target risks. RNAi may be better suited for wasp control in high-value cropping systems due to scaling inefficiencies. Gene drives offer potential for large-scale control but would require legislative and wide social deliberation due to their status as genetic modification. Both RNAi and gene drives will require consultation with tangata whenua. Māori interest groups agreed that exotic wasps must be controlled and expressed aversion to non-targeted traditional control methods. We present a diversity of opinions in parallel with scientific research underscoring the need for continued dialogue with Māori. Novel biotechnological controls must satisfy a broad range of social and cultural criteria, receive regulatory approval, along with being demonstrated as safe, selective, and cost-effective.

The genome sequence of the common wasp, Vespula vulgaris (Linnaeus, 1758)

We present a genome assembly from an individual female Vespula vulgaris (the common wasp; Arthropoda; Insecta; Hymenoptera; Vespidae). The genome sequence is 188 megabases in span. The majority of the assembly is scaffolded into 25 chromosomal pseudomolecules.

Emerging patterns in social wasp invasions

Invasive species are a main driver of biodiversity loss and ecological change globally. Consequently, there is a need to understand how invaders damage ecosystems and to develop effective management strategies. Social wasps (Hymenoptera: Vespidae) include some of the world's most ecologically damaging invasive insects. In recent decades, the invasive social wasp literature has grown rapidly. This may be due in part to increased rate of introduction as well as greater public awareness of invasive wasps and their potential negative impacts on bees. Here, we investigate trends in invasive social wasp research, identifying the emergence of Vespa invasions, the mechanism-based inquiry into Vespula invasions, and the increased application of molecular methods to track invasive species through the invasion process.

A Diverse Viral Community from Predatory Wasps in Their Native and Invaded Range, with a New Virus Infectious to Honey Bees

Wasps of the genus Vespula are social insects that have become major pests and predators in their introduced range. Viruses present in these wasps have been studied in the context of spillover from honey bees, yet we lack an understanding of the endogenous virome of wasps as potential reservoirs of novel emerging infectious diseases. We describe the characterization of 68 novel and nine previously identified virus sequences found in transcriptomes of Vespula vulgaris in colonies sampled from their native range (Belgium) and an invasive range (New Zealand). Many viruses present in the samples were from the Picorna-like virus family (38%). We identified one Luteo-like virus, Vespula vulgaris Luteo-like virus 1, present in the three life stages examined in all colonies from both locations, suggesting this virus is a highly prevalent and persistent infection in wasp colonies. Additionally, we identified a novel Iflavirus with similarity to a recently identified Moku virus, a known wasp and honey bee pathogen. Experimental infection of honey bees with this novel Vespula vulgaris Moku-like virus resulted in an active infection. The high viral diversity present in these invasive wasps is a likely indication that their polyphagous diet is a rich source of viral infections.