Renee L. Corpuz

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 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 to associated research, we generated a chromosome-level genome assembly from a wild-collected female measuring 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.

Hi-C characterizes three-dimensional chromatin organization, facilitates haplotype phasing, and enables genome-assembly scaffolding, but encounters difficulties across complex regions. By coupling chromosome conformation capture (3 C ) with PacBio H iFi long-read sequencing, here we develop a method (CiFi) that enables analysis of genomic interactions across repetitive regions. Starting with as little as 60,000 cells (sub-microgram DNA), the method produces multi-kilobasepair HiFi reads that contain multiple interacting, concatenated segments (~350 bp to 2 kbp). This multiplicity and increase in segment length versus standard short-read-based Hi-C improves read-mapping efficiency and coverage in repetitive regions and enhances haplotype phasing. CiFi pairwise interactions are largely concordant with Hi-C from a human lymphoblastoid cell line, with gains in assigning topologically associating domains across centromeres, segmental duplications, and human disease-associated genomic hotspots. As CiFi requires less input versus established methods, we apply the approach to characterize single small insects: assaying chromatin interactions across the genome from an Anopheles coluzzii mosquito and producing a chromosome-scale scaffolded assembly from a Ceratitis capitata Mediterranean fruit fly. Together, CiFi enables assessment of chromosome-scale interactions of previously recalcitrant low-complexity loci, low-input samples, and small organisms.

Microbial symbionts play crucial roles in host nutrition, defence, and detoxification. However, host‐symbiont interactions are context‐dependent, and environmental stressors can disrupt these benefits. Diverse hosts, including corals, insects and leguminous plants, have been shown to suffer under thermal stress due to the negative impact of high temperatures on their symbionts. This failure is often linked to a symbiont's poor transcriptional regulation of heat shock genes, causing vulnerability at high temperatures. In the bug‐ Caballeronia model system, insect performance at elevated temperatures varies based on the hosted symbiont species. Here, we explore the underlying mechanisms that drive this variation using comparative metatranscriptomics and two symbionts with contrasting host outcomes at high temperatures. We evaluated both host and symbiont transcriptional responses to elevated temperature, testing the hypothesis that symbionts conferring improved host outcomes at high temperatures will have more upregulated heat shock genes under thermal stress compared to those conferring worse host outcomes. Our findings reveal that host transcription did not change with different symbionts but rather only at different temperatures. Furthermore, symbionts had distinct gene expression profiles across temperatures. At 36°C, the heat‐resistant symbiont not only increased expression of heat shock genes but surprisingly upregulated flagellar genes, which are normally turned off during symbiosis. This suggests that symbiont, not host, transcription underlies host benefits at low versus high temperatures and ultimately furthers our understanding of context dependence in the outcomes of symbiotic associations.

Patterns of divergence and speciation on islands have long been of interest in the broader study of evolution. Hawaiʻi’s endemic Kamehameha butterfly ( Vanessa tameamea ) is experiencing population decline, but because of its high vagility and assumed genetic homogeneity as a species, its population structure has not been investigated. To evaluate V. tameamea genetic variation across the Hawaiian Islands, we assembled a reference quality genome assembly for the species using HiFi and HiC reads and performed range-wide population genetic analyses using ddRAD sequencing data. A discriminant analysis of principal components (DAPC) revealed that, contrary to prior assumptions, V. tameamea populations appear to be diverging based on geography, in a pattern similar to other native Hawaiian terrestrial arthropods. Specifically, through demographic history analyses, we find that the distinct population on Kauaʻi is likely to be ancestral, the central islands of Maui, Molokaʻi, and Oʻahu comprise another population, and Hawaiʻi Island forms a third population, with likely more gene exchange with the central islands. Finally, we investigate the SNPs driving differences between groups and find that many are associated with genes that may be relevant to local adaptation to environmental chemicals such as host plant defenses or chemicals introduced by human activity, notably to do with metabolism and detoxification. While much field work remains to investigate any cryptic or phenotypic patterns as well as quantify effective migration, we hope that this work will inform refinement of conservation plans for one of Hawaiʻi’s two native butterflies.

Tephritid fruit flies are invasive species of ripening fruit and vegetables. The olive fly ( Bactrocera oleae ) a specialist of olives, harbors a symbiotic gut bacterium Candidatus Erwinia dacicola , which is crucial to the olive fly’s exploitation of Oleaceae . This study characterized the genome of Ca. E. dacicola to investigate functional pathways that facilitate its obligate symbiosis. We used an extremely high-quality Ca. E. dacicola genome produced in tandem with an olive fly genome and paired that reference with transcriptomics. Of 4,675 genes, 1,783 (38.13%) were classified as pseudogenes. Overall, many pathways are complete, mostly associated with nutritional components. The symbiont also has genes encoding hypothetical proteins to degrade the phenolics in olives. Some pathways were heavily pseudogeneized, suggesting that Ca. E. dacicola have impaired functions in generalized metabolism, carbon utilization, pathogenicity, and signaling systems. Gene selection analyses in Ca. E. dacicola compared to related organisms, indicated positive selection on genes related to amino acid metabolism, carbon utilization, secretion and transport, and energy production. Our results indicate that the main service likely provided by Ca. E. dacicola is the production of amino acids and metabolism of oleuropein. The high pseudogenization rate implies incipient erosion of a formerly free-living symbiont.

Anthurium amnicola is in the monocot family Araceae, subfamily Pothoideae and is a contributing species in Hawaii floriculture industry hybrids. To support future genetic improvements to this commodity, we sequenced and assembled the A. amnicola genome to chromosome-scale using PacBio HiFi and short-read Hi-C sequencing. A total of 98.51% of the 4.79 Gb genome is anchored into 15 chromosomes, with 99.2% gene completeness and a high LTR assembly index (LAI) score of 21.73, indicative of a complete, high-quality assembly. Annotation reveals the presence of 20,380 protein-coding genes, with 78.52% of the genome composed of repetitive sequences, predominantly long terminal repeat retrotransposons (LTR-RT). Phylogenetic analysis identified evolutionary relationships between A. amnicola and representative species in the Araceae and other plant families. This study provides the first reference genome sequence for the neotropical genus Anthurium and insights into Araceae evolution, benefiting the floriculture industry and evolutionary studies.

The remarkable diversity of insect pigmentation offers a captivating avenue for studying evolution and genetics. In tephritids, understanding the molecular basis of mutant traits is also crucial for applied entomology, enabling the creation of genetic sexing strains through genome editing, thus facilitating sex-sorting before sterile insect releases. Here, we present evidence from classical and modern genetics showing that the black pupae (bp) phenotype in the GUA10 strain of Anastrepha ludens is caused by a large deletion at the ebony locus, removing the gene’s entire coding region. Targeted knockout of ebony induced analogous bp phenotypes across six major tephritid agricultural pests, demonstrating that disruption of Ebony alone is sufficient to produce the mutant trait in distantly related species. This functional characterization further allowed a deeper exploration of Ebony’s role in pigmentation and development across life stages in diverse species. Our findings offer key insights for molecular engineering of sexing strains based on the bp marker and for future evolutionary developmental biology studies in tephritids.

The Mexican fruit fly, Anastrepha ludens, is a polyphagous true fruit fly (Diptera: Tephritidae) considered one of the most serious insect pests in Central and North America to various economically relevant fruits. Despite its agricultural relevance, a high-quality genome assembly has not been reported. Here, we described the generation of a chromosome-level genome for the A. ludens using a combination of PacBio high fidelity long-reads and chromatin conformation capture sequencing data. The final assembly consisted of 140 scaffolds (821 Mb, N50 = 131 Mb), containing 99.27% complete conserved orthologs (BUSCO) for Diptera. We identified the sex chromosomes using three strategies: 1) visual inspection of Hi-C contact map and coverage analysis using the HiFi reads, 2) synteny with Drosophila melanogaster, and 3) the difference in the average read depth of autosomal versus sex chromosomal scaffolds. The X chromosome was found in one major scaffold (100 Mb) and eight smaller contigs (1.8 Mb), and the Y chromosome was recovered in one large scaffold (6.1 Mb) and 35 smaller contigs (4.3 Mb). Sex chromosomes and autosomes showed considerable differences of transposable elements and gene content. Moreover, evolutionary rates of orthologs of A. ludens and Anastrepha obliqua revealed a faster evolution of X-linked, compared to autosome-linked, genes, consistent with the faster-X effect, leading us to new insights on the evolution of sex chromosomes in this diverse group of flies. This genome assembly provides a valuable resource for future evolutionary, genetic, and genomic translational research supporting the management of this important agricultural pest.

The implementation of a new genomic assembly pipeline named only the best (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The primary objective of otb is to streamline the process of creating a HiFi/HiC genome, aiming to minimize the manual intervention required in the genome assembly process. The 2-lined spittlebug, (Prosapia bicincta, Hemiptera: Cercopidae), a true bug insect herbivore, serves as a practical test case for evaluating otb. The 2-lined spittlebug is both a crucial agricultural pest and a genomically understudied insect belonging to the order Hemiptera. This insect is a significant threat to grasslands and pastures, leading to plant wilting and phytotoxemia when infested. Its presence in tropical and subtropical regions around the world poses a long-term threat to the composition of plant communities in grassland landscapes, impacting rangelands, and posing a substantial risk to cattle production.