Biology subjects

Geib, S. M.

Publications and source records attributed to Geib, S. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome assembly of the Olympia oyster (Ostrea lurida), the only oyster species native to the West Coast of North America

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 mantles 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.

genomics↗

bioRxiv2026

The chromosome level genome of the Blueberry Stem Gall Wasp, Hemadas nubilipennis (Hymenoptera: Ormyridae) on lowbush blueberry (Vaccinium angustifolium) reveals repeat-driven expansion

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.

genomics↗

bioRxiv2026

Multiple roads to swarming: divergent molecular machineries drive the repeated evolution of locusts

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.

evolutionary biology↗

bioRxiv2026

Highly contiguous genomes of Rhodnius prolixus and Triatoma rubida reveal the molecular basis of haematophagy evolution in Triatominae

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 summaryKissing 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.

evolutionary biology↗

bioRxiv2026

Genome sequencing and multi-stage, blood-feeding, and tissue-specific transcriptome atlas of the Rocky Mountain wood tick provide a critical resource for this vector

Dermacentor andersoni, the Rocky Mountain wood tick, is an important vector for pathogens impacting human and animal health, including bovine anaplasmosis, Colorado tick fever, and Rocky Mountain spotted fever. A better understanding of the biology of this tick is needed for developing disease prevention and vector control strategies. A reference genome was assembled for D. andersoni using high-fidelity (HiFi) long-read PacBio sequences and Hi-C contact mapping, yielding a contiguous assembly in which most contigs matched one of 11 chromosomes. Genome annotation by the NCBI eukaryotic genome annotation pipeline revealed high gene content completeness, yielding a genome completeness score of 94.0% using the Arachnida ortholog dataset. Following genome sequencing, we identified specific genes involved in blood feeding across a range of tissue types and life stages for D. andersoni. To accomplish this, RNA-seq analysis was used to investigate differential gene expression across most organs in adult, nymphal, and larval D. andersoni before and after feeding. Based on this analysis, we identified several gene groups that are involved in blood feeding. Furthermore, we establish sex- and developmental-stage-specific transcriptional profiles. Collectively, this study advances knowledge of D. andersoni biology and enables the development of strategies to limit the spread of diseases transmitted by this tick.

genomics↗

bioRxiv2026

The ivory:mir-193 non-coding RNA gene controls melanic camouflage in a polymorphic moth

A majority of moths use melanic pigmentation to blend into the visual environment, and some species display genetically controlled color polymorphisms that provide tractable systems for dissecting the genetic basis of camouflage. Here we leveraged the natural polymorphism of Anticarsia gemmatalis moths to map a major-effect gene that controls melanic variation, and study its developmental roles using expression and loss-of-function assays. A genome-wide association mapping identifies the ivory:mir-193 non-coding RNA locus as a major locus of melanic variation, with highly-divergent haplotypes differentiating the Light and Dark morphs. Second, the expression of ivory:mir-193 prefigures the melanic coloration of each morph, and suggests that cis-regulatory variation at this locus determines the difference in adult pattern. Finally, CRISPR disruption of the ivory promoter and mir-193 hairpin region each abolish melanic scale pigmentation, demonstrating that this lnc-pri-miRNA module is required for dark-scale differentiation. These findings corroborate the emerging role of ivory:mir-193 as a key factor in the development of melanic patterning, and highlight its unique propensity to repeatedly drive phenotypic variation of adaptive potential in butterflies and moths. HighlightsO_LIAnticarsia gemmatalis display striking variation in camouflage patterns C_LIO_LIDark vs. Light color polymorphism map to the ivory:mir-193 hotspot locus C_LIO_LIHighly-diverged haplotypes drive morph-specific expression of ivory:mir-193 C_LIO_LIThe miR-193 miRNA is required for melanic scale development C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/707733v2_ufig1.gif" ALT="Figure 1"> View larger version (80K): org.highwire.dtl.DTLVardef@8e491eorg.highwire.dtl.DTLVardef@1628425org.highwire.dtl.DTLVardef@d1b691org.highwire.dtl.DTLVardef@29247b_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2026

Chromosome-level genome assembly of the Erythrina Gall Wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae)

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{square}i. As a foundation to associated research, we generated a chromosome-level genome assembly from a wild-collected female measuring <2 mm. The final assembly consists of five scaffolds representing the five autosomes totaling 399 Mb (N50 = 75.6 Mb) and one 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.

genomics↗

bioRxiv2026

Cryptic Insect Microbiome Compositions Unveiled with Full-Length 16S Sequencing

Insects have interconnected relationships with gut microorganisms which can have impacts on behavior and survival. Understanding foundational ecological principles of the insect-associated microorganisms is important to understand how insects utilize microbes to cope with stress and different environments. Common microbiome surveys of insect microbiomes utilize 16S rRNA sequencing of metagenomic DNA. For amplicon-based surveys of insect microbiome, fragment length and 16S rRNA subunit choice may have unintended biases, and some primer combinations may under-represent genus or species richness. Contemporary solutions target sequencing of the entire 16S rRNA fragment. Here, we illustrate the benefit of full-length 16S rRNA sequencing in improving sample resolution compared to V4 which provides new insight into the gut microbiome community composition of an invasive insect. We evaluated the gut microbiome of mass-reared medfly males (Mediterranean fruit fly, Ceratitis capitata) that were collected across a nine-month sampling period. Full-length 16S rRNA PCR products of samples were prepared into a Kinnex 16S rRNA library, sequenced on a PacBio Revio system, and the resulting HiFi amplicon data was processed into amplicon sequence variants (ASVs). Our findings reveal substantial differences in bacterial compositions across different medfly cohorts when sampling the full-length amplicons which were not detectible when only considering the V4 regions. Strain-level gut microbiome variation were supported with genomes assembled from shotgun metagenomic sequencing. Our findings support that long-read sequencing of full-length 16S rRNA amplicon uncover ecologically important interactions between host and gut microbiomes and serve as a bridge between short-fragment sequencing and shotgun metagenomics.

microbiology↗

bioRxiv2026

Applying PCR cycle autonormalization to improve PacBio full-length 16S rRNA sequencing

The bacterial 16S rRNA gene is widely used to characterize host-associated and environmental microbiomes, most commonly through sequencing short hypervariable regions. Recent improvements in PacBio sequencing chemistry and concatenation approaches can now enable high-throughput, full-length 16S rRNA gene sequencing with high accuracy and depth. However, PCR-induced errors remain a major limitation, particularly for full-length amplicons where error accumulation may be elevated due to a five-fold increase in sequence lengths. These challenges are exacerbated when samples vary widely in microbial biomass, making it difficult to select a single optimal number of PCR cycles. Here, we evaluated the effects of PCR cycle autonormalization on PacBio Kinnex full-length 16S rRNA gene sequencing across seven agriculturally relevant specimen types. We compared conventional PCR protocols (20, 24, and 30 cycles) with an autonormalization approach in which individual reactions were terminated during exponential amplification based on real-time fluorescence thresholds. Autonormalized reactions consistently retained a higher proportion of sequences following denoising and chimera removal, exhibited fewer substitution-based errors, and produced more even read distributions across samples. Meanwhile, overamplified reactions (30 cycles) showed elevated error rates and higher sequence removal, particularly in samples with greatest microbial biodiversity. Importantly, PCR protocol had minimal effects on overall community composition relative to specimen types. These results demonstrate that PCR cycle autonormalization improves data yield for full-length 16S rRNA sequencing while maintaining robust inferences, while facilitating streamlined workflows for heterogeneous samples. ImportanceAmplicon-based sequencing of the 16S rRNA gene is foundational tool in microbiome research, yet PCR amplification remains a major source of technical error. This challenge is magnified for full-length 16S rRNA sequencing and for workflows that process specimen types with widely varying microbial biomass. Selecting a single PCR cycle number can result in under-amplification of samples with low 16S rRNA copies or over-amplification and error accumulation in high-titer samples. Here, we show that PCR cycle autonormalization, implemented using iconPCR, substantially improves PacBio full-length 16S rRNA sequencing by reducing PCR-induced substitution errors and chimeras while maintaining consistent biological inference. Autonormalization also enables blind pooling of amplicons without post-PCR quantification or equimolar normalization, reducing hands-on time and sample loss. These benefits make cycle autonormalization particularly valuable for high-throughput and production-scale sequencing applications handling diverse specimen types.

microbiology↗

bioRxiv2025

An loss of independence: genomic insights into a pest fruit fly-bacterial mutualism

Obligate microbial symbioses are often characterized by streamlined biosynthetic pathways and reduced genomes. The evolutionary process of this reduction first involves an increase in the abundance of non-functional coding genes (pseudogenes) followed by their removal. The olive fruit fly (Bactrocera oleae) harbors an extracellular symbiotic gut bacterium Candidatus Erwinia dacicola, which is crucial to its usage of fruit from the olive genus Olea as a larval food source. In this study, we combined genomics and transcriptomics of Ca. E. dacicola to investigate pathways that facilitate this mutualism. Of 4,675 genes in the Ca. E. dacicola genome, 1,783 were classified as pseudogenes. Some biochemical pathways such as amino acid pathways, biofilm regulator BssS, and 6-phospho-{beta}-glucosidase which are implicated in hydrolyzing oleuropein were complete. However, pathways connected to baseline homeostasis, which would impact cellular functions needed for a bacterium to be free-living, were heavily pseudogenized. Gene selection analyses in Ca. E. dacicola, when compared to related organisms, indicated positive selection on genes related to amino acid metabolism, carbon utilization, transport, and energy production. Our results indicate that Ca. E. dacicola is likely producing amino acids and metabolizing plant phytochemicals. These results reveal that the Ca. E. dacicola genome is undergoing incipient genome erosion in support of an unculturable obligate mutualism. ImportanceMany beneficial bacteria that live inside insects have highly reduced genomes, but little is known about the transitional stages that occur as free-living microbes evolve into obligate symbionts. We show that the olive fruit fly symbiont, Candidatus Erwinia dacicola, retains hallmarks of its plant-associated ancestry while undergoing extensive genome degradation, including the accumulation of mobile DNA elements and inactive genes. At the same time, genes involved in nutrient production, environmental persistence, and host interactions remain functional and are evolving under selection, providing a rare snapshot of how bacterial genomes are reshaped during the evolution of an obligate mutualism. These findings have implications for how obligate gut symbioses are formed and maintained in insect herbivores.

genomics↗

bioRxiv2025

Genome report: chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae)

The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is a specialist of fruits of the genus Olea and is a major pest of commercial olives due to their adverse impacts to olive production. In support of genomic and physiological research of the olive fly, we sequenced, assembled, and annotated two independent genomes, one from a wild-collected male and one from a wild-collected female. The resulting genomes are highly contiguous, collinear, and complete, attesting to the accuracy and quality of both assemblies. In addition to the autosomes captured as single contigs, the X and Y chromosomes were also captured as evidenced by the X chromosome showing diploid coverage in the female assembly compared to haploid coverage in the male assembly and the Y chromosome being entirely absent from the female assembly. These assemblies represent the first full chromosome-level assembly for Olive fly. In addition, a complete genome assembly of a known obligate symbiont to the olive fly, Candidatus Erwinia dacicola, was fully captured. The Ca. E. dacicola we report here is the most contiguous to date, represented with a gapless chromosome and two separate gapless plasmids. These genome assemblies, along with bacterial symbiont assembly, provide foundational resources for future genetic and genomic research in support of its management as an agricultural pest.

genomics↗

bioRxiv2025

Genome Report: Improved chromosome-level genome assembly of the American cockroach, Periplaneta americana

1The American cockroach, Periplaneta americana, is a cosmopolitan insect notorious for thriving among humans undeterred by attempts to eliminate it. The traits that contribute to its ubiquity as an opportunistic pest, such as long lifespan, expansive neurosensory capacity, and nutritional flexibility, also make P. americana an excellent invertebrate model organism with a long history in neuroscience and physiological research. Current genetic resources available for P. americana highlight its large, complex genome and richly diverse transcriptional capabilities, but fall short of producing a complete, chromosome-level genome. Here, we present a high-quality de novo genome assembly of a laboratory-raised adult female P. americana using a combination of high fidelity PacBio long reads and Hi-C sequencing. The final 3.23 Gb genome was assembled with chromosomal resolution into 17 scaffolds, consistent with previous karyotype analysis, and has a scaffold N50 of 188.1 Mb and genome BUSCO score of 99.7%. This assembly includes a chromosome that was missing from the previous reference genome for this species. Protein prediction and annotation were performed via the NCBI Eukaryotic Genome Annotation Pipeline, which identified 16,780 protein-coding genes and generated an annotation BUSCO score of 97.8%. Ortholog comparisons with available Blattodea assemblies highlight the expanded chemosensory and immune capabilities of P. americana compared to termite relatives. This genome assembly is a valuable tool for facilitating future research on the biology and evolution of this remarkable insect.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of Protandrena (Anthemurgus) passiflorae (Hymenoptera: Andrenidae), a host-plant specialist bee

The passion flower bee, Protandrena (Anthemurgus) passiflorae (Robertson) is a monolectic, host-plant specialist of the passionflower plant Passiflora lutea L. Using a single adult male individual, we generated long-read PacBio HiFi, HiC, and short-read RNA sequencing data to build a well-annotated, chromosome-level genome assembly for this species. The final nuclear genome is 249 Mb with 150x coverage and with most of the genome scaffolding into 12 chromosomes. The scaffold N50 is 21.4 Mb and the genome has a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 97.2% for 5991 hymenopteran genes. BRAKER3 annotation of the genome identified 12,098 genes and 15,353 total transcripts and found that 20.27% of the genome is made up of repetitive elements. We resolved a mitochondrial genome of 12.7 kb. The P. passiflorae genome represents one of only a few published andrenid bee genomes and one of the first monolectic bees. This new high-quality genome will serve as a valuable resource for investigating the genomic basis of specialization and for providing a useful resource for studying pollinator health and conservation.

genomics↗

bioRxiv2025

CiFi: Accurate long-read chromatin conformation capture with low-input requirements

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 (3C) with PacBio HiFi 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.

genomics↗

bioRxiv2025

From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives

The yellow fever mosquito (Aedes aegypti) is an organism of high medical importance because it is the primary vector for diseases such as yellow fever, Zika, dengue, and chikungunya. Its medical importance has made it a subject of numerous efforts to understand their biology. One such effort, was the development of a high-quality reference genome (AaegL5). However, this reference genome was sourced from a highly inbred laboratory strain with unknown geographic origin. Thus, the reference is not representative of a wild mosquito, let alone one from its native range in sub-Saharan Africa. To better understand the genetic architecture of Ae. aegypti and their sister species, we developed two de novo chromosome-scale genomes with sequences sourced from single individuals: one of Ae. aegypti formosus (Aaf) from Burkina Faso and one of Ae. mascarensis (Am) from Mauritius. Both genomes exhibit high contiguity and gene completeness, comparable to AaegL5. While Aaf exhibits high degree of synteny to AaegL5, it also exhibits several large inversions. We further conducted comparative genomic analyses using our genomes and other publicly available culicid reference genomes to find extensive chromosomal rearrangements between major lineages. Overrepresentation analysis of expanded genes in Aaf, AaegL5, and Am revealed that while the overarching category of genes that have expanded are similar, the specific genes that have expanded differ. Our findings elucidate novel insights into chromosome evolution at both microevolutionary and macroevolutionary scales. The genomic resources we present are additions to the arsenal of biologists in understanding mosquito biology and genome evolution. SignificanceAedes aegypti is a major arboviral disease vector found throughout the tropics and sub-tropics. Its subspecies differ ecologically, as native sub-Saharan African form feeds on mammals generally and inhabit both sylvatic and domestic areas and the global invasive form preferentially feeds on humans and lives primarily domestic areas. Their medical importance has prompted the development of a high-quality reference genome, but it was sourced from an inbred laboratory strain of unknown origin. Here, we leveraged PacBio HiFi sequencing and HiC sequencing to develop the first de novo genome of Ae. aegypti sampled its native range in Burkina Faso. We also present a de novo genome of Ae. mascarensis, its sister species. Our genomes are comparably contiguous and complete to the reference genome. Comparative genomic analysis using our genomes and other culicid reference genomes reveal extensive chromosomal rearrangements.

genomics↗

bioRxiv2024

Utilizing full-length 16S rRNA sequencing to assess the impact of diet formulation and age on targeted gut microbiome colonization in laboratory and mass-reared Mediterranean fruit flies

Insect gut microbiomes have important roles in overall host health and how hosts function in the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, like the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to colonize hosts is an important for the establishment of lost or novel microbiota into mass-reared insects. The goal of this study was to evaluate how host age and diet inoculation method influenced bacterial establishment in laboratory and mass-reared medfly. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio 16S rRNA sequencing to track the establishment of a specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. Host medfly fed a liquid diet with the target bacteria were able to be colonized regardless of age, but those fed a slurry-based diet and separate water source were more resilient. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain, but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects. ImportanceInsects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goals of our study were to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species throughout the world. Mass-reared insects for sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medfly. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity of that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

microbiology↗

bioRxiv2024

Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee

Comparative genomic studies of social insects suggest that changes in gene regulation are associated with evolutionary transitions in social behavior, but the activity of predicted regulatory regions has not been tested empirically. We used STARR-seq, a high-throughput enhancer discovery tool, to identify and measure the activity of enhancers in the socially variable sweat bee, Lasioglossum albipes. We identified over 36,000 enhancers in the L. albipes genome from three social and three solitary populations. Many enhancers were identified in only a subset of L. albipes populations, revealing rapid divergence in regulatory regions within this species. Population-specific enhancers were often proximal to the same genes across populations, suggesting compensatory gains and losses of regulatory regions may preserve gene activity. We also identified 1182 enhancers with significant differences in activity between social and solitary populations, some of which are conserved regulatory regions across species of bees. These results indicate that social trait variation in L. albipes is driven both by the fine-tuning of ancient enhancers as well as lineage-specific regulatory changes. Combining enhancer activity with population genetic data revealed variants associated with differences in enhancer activity and identified a subset of differential enhancers with signatures of selection associated with social behavior. Together, these results provide the first empirical map of enhancers in a socially flexible bee and highlight links between cis-regulatory variation and the evolution of social behavior.

evolutionary biology↗

bioRxiv2024

The genetic basis of the black pupae phenotype in tephritid fruit flies

The remarkable diversity of insect pigmentation offers a captivating avenue for exploring evolution and genetics. In tephritid fruit flies, decoding the molecular pathways underlying pigmentation traits also plays a central role in applied entomology. Mutant phenotypes like the black pupae (bp) have long been used as a component of genetic sexing strains, allowing male-only release in tephritid sterile insect technique applications. However, the genetic basis of bp remains largely unknown. Here, we present independent evidence from classical and modern genetics showing that the bp phenotype in the GUA10 strain of the Mexican fruit fly, Anastrepha ludens, is caused by a large deletion at the ebony locus resulting in the removal of the entire protein-coding region of the gene. Targeted knockout of ebony induced analogous bp phenotypes across six tephritid species spanning over 50 million years of divergent evolution. This functionally validated our findings and allowed for a deeper investigation into the role of Ebony in pigmentation and development in these species. Our study offers fundamental knowledge for developing new sexing strains based on the bp marker and for future evolutionary developmental biology studies in tephritid fruit flies.

genomics↗