J. Spencer Johnston

Adaptive and neutral processes have produced a spectrum of genome sizes across organisms. Amphibians in particular possess a wide range in C-values, from Phyllobates and Hyloxalus , which respectively possess species with the largest (13.0 pg) and second smallest (2.6 pg) genomes in the family. Phylogenetically controlled regression analyses indicate that genome size is positively correlated with snout-vent-length, oocyte number, and clutch size, but negatively correlated with active metabolic rate and metabolic scope. While body size and metabolic rate are also correlates of toxicity, we found no relationship between genome size and evolution of chemical defense within Dendrobatidae. Genome size evolution in Dendrobatidae provides insight into the processes shaping genome size evolution over short timescales and establishes a novel system in which to study the mechanistic links between genome size and organismal physiology.

Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.

The red imported fire ant Solenopsis invicta Buren (fire ant hereafter) is a global pest that inflicts billions of dollars in damages to the United States economy and poses a major threat on a global scale. Concerns with the broad-spectrum application of insecticides have facilitated the hunt for natural enemy-mediated controls. One of these, the virus Solenopsis invicta virus-3 (SINV-3 hereafter) is exceptionally virulent in laboratory settings. However, despite high mortality rates in the laboratory and documented widespread SINV-3 prevalence in the southern United States, the fire ant remains a major pest. To explore this paradox, we document the immune response elicited by the fire ant when infected with SINV-3. We sequence the fire ant transcriptome prior to and following infection with SINV-3, and identify and discuss in detail genes in immune response pathways differentially expressed following infection with SINV-3. This information provides insights into genes and pathways involved in the SINV-3 infection response in the fire ant and offers avenues to pursue, to suppress key immune response genes and force the fire ant to succumb to SINV-3 infection in the field.

The house cricket, Acheta domesticus , is one of the most farmed insects worldwide and the foundation of an emerging industry for the use of insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of recent reports on climate change and biodiversity loss largely driven by agriculture. As with other agricultural crops, genetic resources are needed to improve crickets for food and other applications. We present the first high quality annotated genome assembly of A. domesticus which was assembled from long read data and scaffolded to chromosome level from long range data, providing information on promoters and genes needed for genetic manipulation. Gene groups that may be useful for improving the value of these insects to farmers were manually annotated, mainly genes related to immunity. Metagenome scaffolds in the A. domesticus assembly, including those from bacteria, other microbes and viruses such as Invertebrate Iridescent Virus 6 (IIV6), were submitted in a separate accession as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of selected genes and discuss implications for the food, pharmaceutical and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene to produce a useful white-eye biomarker phenotype. We are utilizing these data to develop base technologies and methodologies for downstream commercial applications, including the generation of more nutritious and disease resistant crickets as well as lines producing valuable bioproducts such as vaccines and antibiotics. We also discuss how this foundational research can play a critical role in utilizing the largest, most diverse yet almost entirely untapped biological resource on Earth: Class Insecta. Significance Statement: Sequencing and assembly of the genome of the house cricket has led to improvements in farmed insects for food, pharmaceutical and other applications.

The lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), is a major global pest of cereal grains. Infestations are difficult to control as larvae feed inside grain kernels, and many populations are resistant to both contact insecticides and fumigants. We sequenced the genome of R. dominica to identify genes responsible for important biological functions and develop more targeted and efficacious management strategies. The genome was assembled from long read sequencing and long-range scaffolding technologies. The genome assembly is 479.1 Mb, close to the predicted genome size of 480.4 Mb by flow cytometry. This assembly is among the most contiguous beetle assemblies published to date, with 139 scaffolds, an N₅₀ of 53.6 Mb, and L₅₀ of 4, indicating chromosome-scale scaffolds. Predicted genes from biologically relevant groups were manually annotated using transcriptome data from adults and different larval tissues to guide annotation. The expansion of carbohydrase and serine peptidase genes suggest that they combine to enable efficient digestion of cereal proteins. A reduction in the copy number of several detoxification gene families relative to other coleopterans may reflect the low selective pressure on these genes in an insect that spends most of its life feeding internally. Chemoreceptor genes contain elevated numbers of pseudogenes for odorant receptors that also may be related to the recent ontogenetic shift of R. dominica to a diet consisting primarily of stored grains. Analysis of repetitive sequences will further define the evolution of bostrichid beetles compared to other species. The data overall contribute significantly to coleopteran genetic research.

The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the diversity of food diet is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptors expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the active dynamic of gustatory receptor evolution in Spodoptera spp . We first sequenced de novo the full 465Mb genome of S. littoralis , and manually annotated all chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.

Dramatic genome size variation exists across the Tree of Life. Some crustacean groups, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that genome sizes may be constrained due to physiological pressures. This may indicate that a general “genome-temperature-size” rule exists in ectotherms, in which body-size and latitude may be predictive of genome size. We examined the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncovered a 6-fold genome size variation within Haustoriidae, a substantial amount considering this clade is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. We also found evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays.

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map

The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalizations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed these data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes, and that orders exhibit striking differences in rates of fusions, fissions and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups.

Genome sizes vary by orders of magnitude across the Tree of Life and lack any correlation with organismal complexity. Some crustacean orders, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that natural selection may constrain genome sizes due to physiological pressures. In this study, we examine the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncover a 6-fold genome size variation within a clade that is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. Finally, we find evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays. Significance Statement: The evolution of genome size has been a long-standing puzzle in biology. In this work, we find that genome sizes may be driven by different selection regimes following shifts to a new habitat. Dramatic genome size changes can occur rapidly, in only a few million years. Data Availability Statement: Raw data sheets have been deposited on Dryad: SUBMITTED. Raw sequence reads are available at from NCBI under Bioproject SUBMITTED.