Sheina B. Sim

Eurosta solidaginis is a plant-parasitic insect that develops from egg to adult inside of a spheroid gall it induces on the stem of goldenrod plants (Solidago spp.). E. solidaginis is widespread across North America, with a geographic distribution that extends from Southern Canada to Texas and the Southern U.S. and from the Atlantic coast to the Great Plains and includes scattered populations reaching the West coast. The natural history, ecology and physiology of E. solidaginis are well-documented, and its overwintering physiology, multitrophic interactions, and ecological speciation have been well-studied. Surprisingly, genomic resources are restricted to an incomplete scaffold-level genome assembly lacking protein-coding gene annotation. To advance understanding of the physiology, gall-forming, and population structure of E. solidaginis, we sequenced and assembled the genome of a single pupa using PacBio HiFi sequencing and Hi-C chromatin proximity sequencing technology. Here, we present a fully-annotated, chromosome-level de novo assembly of the 1.9 Gb genome, spanning five autosomes and the sex chromosomes. The assembly has a contig N50 of 3.7 Mb and a scaffold N50 of 289.3 Mb, and 96.5% of expected Diptera BUSCOs in the genome found in single copy. We annotated 14,223 identified protein-coding genes, identifying 96.2% of BUSCOs in the protein set found in single copy. The 18,293 bp mitochondrial genome was assembled and subsequently annotated separately. Even though there are 400-450 gall-inducing tephritid species, this is the second high-quality, chromosome-level genome assembly of a gall-forming fly in the family, and the third freeze tolerant dipteran genome.

The Olympia oyster ( Ostrea lurida ) was once a major food source and a key component of coastal marine ecosystems and culture on the US West Coast. Overfishing and habitat contamination in the early to mid-20th century severely depleted populations of Olympia oysters, and the species is currently considered a species of concern. Although multiple restoration efforts are underway, progress understanding the species biology and recovery potential has been limited by the historical lack of genomic resources. Here, we report a chromosome-level assembly of the Olympia oyster. The assembly was built using Oxford Nanopore reads and Hi-C to obtain a highly contiguous 1.03 Gb-assembly consisting of 10 chromosomes. RNA from gills, mantle, adductor muscle, and a mix of brooding eggs and larvae were also sequenced as 150 nt long paired-end reads which were used to guide the genome annotation. Over 52 K genes were predicted in the genome, of which 34K were protein-coding. A BUSCO analysis on the assembly showed 98.9% of the mollusca_odb12 gene set were complete (with 2.1% duplicated, and 0.8% missing). The short RNA reads were also used to identify tissue-level gene expression signatures in adductor muscles, egg and brooding larvae, and mantle. Development-related genes were highly expressed in eggs and brooding larvae whereas many xenobiotic metabolism genes were present in mantle tissues, highlighting mantle’s role in the interaction of the oyster with external environments. This new genomic resource will greatly advance our understanding of this keystone mollusk and provide a critical tool for guiding restoration efforts and the development of sustainable commercial production.

Gall-inducing wasps are emerging models for studying plantinsect coevolution, host manipulation, host plant adaptation, and speciation, yet chromosome-level resources remain scarce for most lineages. The blueberry stem gall wasp (BSGW), Hemadas nubilipennis (Hymenoptera: Ormyridae), is native to North America where it induces galls on both lowbush (Vaccinium angustifolium) and highbush blueberries (V. corymbosum). Recently, BSGW has reached outbreak densities in cultivated highbush production. Given that (a) the biology has been characterized primarily from natural lowbush-associated populations, (b) the absence of genomic resources limits comparative analyses, and (c) populations on cultivated highbush represent a recent host shift, we generated the first chromosome-level genome from wild lowbush blueberry. The BSGW genome consists of five chromosome-scale scaffolds totaling 1.08 Gb (N50 = 218 Mb), the second largest known in Chalcidoidea. Comparative analysis reveals that genome size variation is driven primarily by transposable element proliferation (R = 0.96, p < 0.001), with BSGW exhibiting a high proportion of unclassified TEs. Gene-body methylation is conserved, enriched in exons of broadly expressed core genes, and correlates with gene density. The mitochondrial genome (18,697 bp) exhibits extensive gene rearrangement, and COI sequences reveal 4.35.4% divergence from geographically distant populations, suggesting a complex of cryptic species. Additionally, we assemble a near-complete genome of the endosymbiont Wolbachia pipientis (Supergroup A), which encodes PifA and PifB effectors potentially linked to parthenogenesis. These resources establish a foundation for population genomics, taxonomic revision, and applied management, while providing insights into genome architecture, epigenetics, and symbiont interactions.

Diabrotica undecimpunctata ssp. howardi, the southern corn rootworm or eastern 12-spotted cucumber beetle, is a generalist insect herbivore that causes damage and yield loss to several crops in North America, including maize. Unresolved phylogenetic relationships within and among D. undecimpunctata subspecies are impacting current quarantine policies. We report the chromosome-level haploid genome assembly, icDiaUnde3, constructed using HiFi and Hi-C read data from a single male D. undecimpunctata collected and identified as subspecies howardi based on geographic location and morphology. The primary 1.74 Gbp assembly contains 11 chromosome-length scaffolds representing 9 autosomes, a single X chromosome, and a supernumerary (B) chromosome (scaffold N50 = 162.8 Mb and L50 = 5). Ab initio and evidence-based structural reference sequence (RefSeq) annotations predicted 18,959 protein-coding genes, in which 99.2% of the 1,367 Benchmark Universal Single-Copy Orthologs from Insecta were complete. Repeat elements occupy 1.26 Gbp (72.33%) of the icDiaUnde3 assembly, with nearly 36% predicted to be retroelements. Alignment of whole chromosomes from icDiaUnde3 with those previously assembled from Diabrotica spp. predicted 2 and 6 autosomal inversions with D. balteata and D. virgifera, respectively. The mitochondrial genome had an annotated gene order and orientation conserved among beetles. The icDiaUnde3 reference genome assembly is a vital resource for taxonomic, comparative, and functional studies to enhance sustainable crop production.

Locust swarming, one of nature's most spectacular examples of a repeated emergent polyphenism, has long been suspected to rely on conserved "swarming genes" or shared genomic features. By applying a model-clade approach comparing six species that vary in their degrees of plasticity and collective behavior, we show that the evolution of swarming locusts is not driven by shared genomic features or a universal set of swarming genes. In contrast, we find that this phenomenon evolved through flexible regulatory architectures, in which the degree of behavioral plasticity directly correlates with the total scale of density-responsive gene expression. While different locust species recruit largely non-overlapping gene sets to achieve the same syndrome, these divergent molecular machineries converge on similar higher-level biological functions. Thus, multiple molecular pathways achieve locust swarming, challenging the preconceived notion about the genetic prerequisites to transition from solitary to collective states. Further, we establish that a complex syndrome such as locust swarming emerges through modular regulatory systems that can be amplified, modified, or attenuated across the tree of life.

Insects of the subfamily Triatominae, commonly known as kissing bugs, are obligate blood-feeding vectors of Trypanosoma cruzi , the causative agent of Chagas disease. Rhodnius prolixus is among the most epidemiologically important vectors in Latin America, whereas Triatoma rubida frequently invades homes and is a potential vector in the southern United States and northern Mexico. Triatomines likely evolved from predatory reduviid assassin bugs through a transition from feeding on arthropods associated with vertebrate hosts to feeding directly on vertebrate blood. To investigate the genomic basis of this ecological and dietary shift, we generated highly contiguous, near chromosome-level genome assemblies and structural gene annotations for R. prolixus and T. rubida . The new R. prolixus assembly improves scaffold N50 more than 40-fold over the current reference genome, from 1.1 to 43.9 Mb, while reducing assembly gaps by several orders of magnitude. Both assemblies exceed 97% BUSCO completeness. Comparative analyses with representative hemipteran genomes revealed expansions of gene families associated with chemosensation and metabolism, including detoxification, protein degradation, and digestion, together with signatures of positive selection in genes involved in digestive and sensory functions. These assemblies represent the most contiguous and complete genomic resources available for Triatominae and provide a robust foundation for investigating vector biology, host adaptation, and the evolutionary origins of blood feeding within Reduviidae. Interpretive summary: Kissing bugs are insects that are known for feeding on blood. They can spread a disease called Chagas disease because they transmit a parasite called Trypanosoma cruzi . To understand how kissing bugs evolved and which genes facilitate blood feeding of vertebrates, a collaboration between scientists at USDA-ARS, University of Georgia, and University of South Bohemia sequenced the genome of two kissing bugs: Rhodnius prolixus and Triatoma rubida . By comparing the genes with those of other insects in the order Hemiptera, scientists discovered that kissing bugs have more genes involved with detecting environmental chemical stimuli and metabolism as well as positive selection for genes involved with digestion and sensory-related proteins. These genome assemblies will help scientists learn more about how these insects evolved, and this research is important for understanding insect feeding biology which can be used to develop methods to control the kissing bugs and the spread of Chagas disease.

The Erythrina gall wasp, Quadrastichus erythrinae, is an invasive gall-inducing chalcidoid wasp and a major pest of the endemic wiliwili tree (Erythrina sandwicensis) in Hawai’i. As a foundation for associated research, we generated a chromosome-level genome assembly from a wild-collected female measuring <2 mm. The final assembly consists of 5 scaffolds representing the 5 autosomes totaling 399 Mb (N50 = 75.6 Mb) and 1 unplaced 16 kb contig. BUSCO analysis recovers 91.1% of conserved Hymenoptera orthologs, representing the first chromosome-scale genome for the genus Quadrastichus. Comparative genomic analyses reveal syntenic conservation across Hymenoptera despite deep evolutionary divergence, with strongest collinearity to the chalcidoid Nasonia vitripennis. Genome size variation is largely explained by repeat content, and Q. erythrinae exhibits high proportions of unclassified transposable elements similar to the cynipid gall inducer. We also assembled a complete genome of its endosymbiont, Wolbachia pipientis. Together, these genomic resources provide a foundation for comparative, evolutionary, and applied research aimed at managing this invasive pest.

The pecan weevil, Curculio caryae (Horn), is an obligate feeder of pecan and native hickory trees (genus Carya ) throughout North America. Subsequently it is a significant agricultural pest in pecan orchards. In this study, we present a reference quality genome using deep-coverage, ~40x PacBio HiFi genome sequence reads, and chromatin confirmation, Hi-C, scaffolding. The final genome assembly is approximately 2.2 Gb, which was confirmed by flow cytometry. The primary genome scaffolds have an N50 of 132 Mb and a BUSCO completeness of 95.4% [S:94.3%, D:1.1%]. Furthermore, we employed PacBio long-read RNA, Iso-seq, for de novo gene annotation, in conjunction with InterProscan to identify approximately 19,000 protein coding genes. Repeat content is extensive, contributing at least >80% of the total genome. This data set provides a valuable resource for comparative genomics and evolutionary studies of an economically impactful group of insect pests that currently lack extensive genomic resources.

The Queensland longhorn beetle (QLB), Acalolepta aesthetica (Olliff), was first detected in the Puna District of Hawai’i Island in 2009 and has since been observed to attack high value specialty crops such as cacao (Theobroma cacao), breadfruit (Artocarpus altilis), and citrus (Citrus spp.), as well as the culturally important kukui, Aleurites moluccanus. Endemic to the Australian states of Queensland and New South Wales, QLB had no pest status before introduction into Hawai’i. To address the lack of basic biological data on QLB, we conducted four pilot experiments to support pest management efforts. These included sequencing the CO1 region of the mitochondrial genome, observing beetle behavior in both a laboratory wind tunnel during scotophase and in the field using harmonic radar tracking, and obtaining QLB spatial distribution data through a citizen science web-based reporting application hosted by ArcGIS Online. Our results place QLB in a phylogenetic context, which will allow the development of diagnostic tools to differentiate QLB from other longhorn beetles. Behavioral observations suggest that QLB are largely sedentary, move mostly by walking with rare flights, and spend most of their time in trees. Citizen science reports suggest QLB populations are highest in May-July, beetle locations are largely restricted to elevations under 500 m, and population expansions are mostly occurring along the coast. These data combined can be applied to pest management efforts for this important and invasive agricultural pest. Further, we hope this interdisciplinary approach can serve as a framework for research response efforts to invasive insects generally.

The New World screwworm, Cochliomyia hominivorax, is an obligate parasite of warm-blooded animals and a major pest of livestock and wildlife in the Americas. The first genome assembly for C. hominivorax enabled substantial progress in key areas including gene expression related to fly behavior and physiology and gene editing technologies. However, the first genome was sequenced prior to several technological advances that result in fewer errors and better genome annotations. Here, we used the trio-binning approach to produce haplotype-resolved genome assemblies of C. hominivorax. A single male progeny from the cross of a Panama line male with a production strain female was sequenced using PacBio HiFi and scaffolded using Hi-C chromatin conformation, while Illumina NextSeq 2000 was used for short-read sequencing of both parents to facilitate trio-binning. We produced a linear haploid reference assembly by transferring a copy of the X chromosome and mitochondrial genome to the paternal haplotype. This assembly is comprised of 5 autosomes, 2 sex chromosomes, the mitogenome, and 75 unplaced scaffolds spanning 455.6 Mb, which is closer to the predicted size based on flow cytometry (443.8 Mb) than the previous assembly of 534.4 Mb. NCBI's external Eukaryotic Genome Annotation Pipeline (EGAPx) was used to annotate the protein-coding and non-coding genes in the linear haploid reference and the maternal haplotype assemblies. Due to the better resolution of the sex chromosomes and updated genome annotations, these improved assemblies will advance future experiments aimed at understanding sex determination, gene expression, and the evolution of parasitism in the Calliphoridae.