The Genome of the Yellow Mealworm, Tenebrio molitor: It's Bigger Than You Think.

BACKGROUND: Insects are a sustainable source of protein for human food and animal feed. We present a genome assembly, CRISPR gene editing, and life stage-specific transcriptomes for the yellow mealworm, Tenebrio molitor, one of the most intensively farmed insects worldwide. METHODS: Long and short reads and long-range data were obtained from a T. molitor male pupa. Sequencing transcripts from 12 T. molitor life stages resulted in 279 million reads for gene prediction and genetic engineering. A unique plasmid delivery system containing guide RNAs targeting the eye color gene vermilion flanking the muscle actin gene promoter and EGFP marker was used in CRISPR/Cas9 transformation. RESULTS: The assembly is approximately 53% of the genome size of 756.8 ± 9.6 Mb, measured using flow cytometry. Assembly was complicated by a satellitome of at least 11 highly conserved satDNAs occupying 28% of the genome. The injection of the plasmid into embryos resulted in knock-out of Tm vermilion and knock-in of EGFP. CONCLUSIONS: The genome of T. molitor is longer than current assemblies (including ours) due to a substantial amount (26.5%) of only one highly abundant satellite DNA sequence. Genetic sequences and transformation tools for an insect important to the food and feed industries will promote the sustainable utilization of mealworms and other farmed insects.

Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture.

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.

Transcriptome analysis of life stages of the house cricket, Acheta domesticus, to improve insect crop production.

To develop genetic resources for the improvement of insects as food, we sequenced transcripts from embryos, one-day hatchlings, three nymphal stages, and male and female adults of the house cricket, Acheta domesticus. A draft transcriptome was assembled from more than 138 million sequences combined from all life stages and sexes. The draft transcriptome assembly contained 45,866 contigs, and more than half were similar to sequences at NCBI (e value < e-3). The highest sequence identity was found in sequences from the termites Cryptotermes secundus and Zootermopsis nevadensis. Sequences with identity to Gregarina niphandrodes suggest that these crickets carry the parasite. Among all life stages, there were 5,042 genes with differential expression between life stages (significant at p < 0.05). An enrichment analysis of gene ontology terms from each life stage or sex highlighted genes that were important to biological processes in cricket development. We further characterized genes that may be important in future studies of genetically modified crickets for improved food production, including those involved in RNA interference, and those encoding prolixicin and hexamerins. The data represent an important first step in our efforts to provide genetically improved crickets for human consumption and livestock feed.

Self-selection of food ingredients and agricultural by-products by the house cricket, Acheta domesticus (Orthoptera: Gryllidae): A holistic approach to develop optimized diets.

The house cricket, Acheta domesticus L. (Orthoptera: Gryllidae) is one of the most important species of industrialized insects in the United States. Within the past five years the market of cricket powder as a food ingredient has been growing with increasing consumer interest on more sustainable sources of food. However, high labor costs of cricket production and high prices of cricket feed formulations result in cricket powder market prices much higher than other protein-rich food ingredients, making cricket powder only competitive within the novelty food market. In this study new diets formulated using by-products were developed using dietary self-selection followed by regression analysis. Crickets selected among seven different combinations of ingredients. Consumption ratios of food ingredients and by-products were used to determine macro and micro-nutrient intake. Regression analysis was used to determine the individual nutrient intake effect on cricket biomass production. Intake of vitamin C, sterol, manganese, and vitamins B1 and B5 had the most significant impact on live biomass production. Four diets were formulated based on this information and compared with a reference (Patton's 13) and a commercial diet. Although, crickets reared on Patton's diet 13 produced the most dry-weight biomass and developed the fastest, diet 4 (consisting of 92% by-products) generated the most profit (with a cost of $0.39 USD per kg) after an economic analysis that did not include the commercial formulation. Dry-weight biomass production was not significantly different among the four new diets and the commercial diet. This study demonstrated the value of dietary self-selection studies in developing oligidic insect diets and in studies of insect nutrition. This is the first such study involving farmed edible crickets and agricultural by-products. Four new cricket diet formulations contain between 62 and 92% agricultural by-products are included.

Verification of Argentine ant defensive compounds and their behavioral effects on heterospecific competitors and conspecific nestmates.

The invasive Argentine ant (Linepithema humile) has become established worldwide in regions with Mediterranean or subtropical climates. The species typically disrupts the balance of natural ecosystems by competitively displacing some native ant species via strong exploitation and interference competition. Here we report that Argentine ants utilize glandular secretions for inter and intra-specific communications during aggressive interactions with a heterospecific competitor, California harvester ant (Pogonomyrmex californicus). Chemical analyses indicated that Argentine ants deploy glandular secretions containing two major volatile iridoids, dolichodial and iridomyrmecin, on the competitor's cuticular surface during aggressive interactions. Bioassays indicated that the glandular secretions function as a defensive allomone, causing high levels of irritation in the heterospecific. Furthermore, the same glandular secretions elicited alarm and attraction of conspecific nestmates, potentially enabling more rapid/coordinated defense by the Argentine ants. Two major volatile constituents of the glandular secretion, dolichodial and iridomyrmecin, were sufficient to elicit these responses in conspecifics (as a mixture or individual compounds). The current study suggests that invasive Argentine ants' superior exploitation and interference competition may rely on the species' effective semiochemical parsimony.

Sex Attractant Pheromone of the Luna Moth, Actias luna (Linnaeus).

Giant silk moths (Lepidoptera: Saturniidae) typically are not well represented as larvae or adults in community level inventories of Lepidoptera, and as a result, little is known about their population dynamics. Furthermore, in recent years, many species of silk moths appear to have experienced population declines. Volatile sex pheromones are powerful sampling tools that can be used in operational conservation and monitoring programs for insects. Here, we describe the identification of the sex attractant pheromone of a giant silk moth, the luna moth Actias luna. Coupled gas chromatography-electroantennographic detection and gas chromatography-mass spectrometric analyses of extracts from pheromone glands of female luna moths supported the identification of (6E,11Z)-6,11-octadecadienal (E6,Z11-18:Ald), (6E)-6-octadecenal (E6-18:Ald), and (11Z)-11-octadecenal (Z11-18:Ald) as the compounds in extracts that elicited responses from antennae of male moths. These identifications were confirmed by synthesis, followed by testing of blends of the synthetic compounds in field trials in Ontario, Canada, and Kentucky, USA. Male moths were attracted to synthetic E6,Z11-18:Ald as a single component. Attraction appeared to be enhanced by addition of E6-18:Ald but not Z11-18:Ald, suggesting that the luna moth pheromone consists of a blend of E6,Z11-18:Ald and E6-18:Ald.

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection.

Clostridium difficile infection (CDI) is characterized by dysbiosis of the intestinal microbiota and a profound derangement in the fecal metabolome. However, the contribution of specific gut microbes to fecal metabolites in C. difficile-associated gut microbiome remains poorly understood. Using gas-chromatography mass spectrometry (GC-MS) and 16S rRNA deep sequencing, we analyzed the metabolome and microbiome of fecal samples obtained longitudinally from subjects with Clostridium difficile infection (n = 7) and healthy controls (n = 6). From 155 fecal metabolites, we identified two sterol metabolites at >95% match to cholesterol and coprostanol that significantly discriminated C. difficile-associated gut microbiome from healthy microbiota. By correlating the levels of cholesterol and coprostanol in fecal extracts with 2,395 bacterial operational taxonomic units (OTUs) determined by 16S rRNA sequencing, we identified 63 OTUs associated with high levels of coprostanol and 2 OTUs correlated with low coprostanol levels. Using indicator species analysis (ISA), 31 of the 63 coprostanol-associated bacteria correlated with health, and two Veillonella species were associated with low coprostanol levels that correlated strongly with CDI. These 65 bacterial taxa could be clustered into 12 sub-communities, with each community containing a consortium of organisms that co-occurred with one another. Our studies identified 63 human gut microbes associated with cholesterol-reducing activities. Given the importance of gut bacteria in reducing and eliminating cholesterol from the GI tract, these results support the recent finding that gut microbiome may play an important role in host lipid metabolism.

Sex-specific mating pheromones in the nematode Panagrellus redivivus.

Nematodes use an extensive chemical language based on glycosides of the dideoxysugar ascarylose for developmental regulation (dauer formation), male sex attraction, aggregation, and dispersal. However, no examples of a female- or hermaphrodite-specific sex attractant have been identified to date. In this study, we investigated the pheromone system of the gonochoristic sour paste nematode Panagrellus redivivus, which produces sex-specific attractants of the opposite sex. Activity-guided fractionation of the P. redivivus exometabolome revealed that males are strongly attracted to ascr#1 (also known as daumone), an ascaroside previously identified from Caenorhabditis elegans hermaphrodites. Female P. redivivus are repelled by high concentrations of ascr#1 but are specifically attracted to a previously unknown ascaroside that we named dhas#18, a dihydroxy derivative of the known ascr#18 and an ascaroside that features extensive functionalization of the lipid-derived side chain. Targeted profiling of the P. redivivus exometabolome revealed several additional ascarosides that did not induce strong chemotaxis. We show that P. redivivus females, but not males, produce the male-attracting ascr#1, whereas males, but not females, produce the female-attracting dhas#18. These results show that ascaroside biosynthesis in P. redivivus is highly sex-specific. Furthermore, the extensive side chain functionalization in dhas#18, which is reminiscent of polyketide-derived natural products, indicates unanticipated biosynthetic capabilities in nematodes.

Defensive spiroketals from Asceles glaber (Phasmatodea): absolute configuration and effects on ants and mosquitoes.

Insects are the largest and most diverse group of organisms on earth, with over 1,000,000 species identified to date. Stick insects ("walkingsticks" or "phasmids", Order Phasmatodea) are known for and name-derived from their camouflage that acts as a primary line of defense from predation. However, many species also possess a potent chemical defense spray. Recently we discovered that the spray of Asceles glaber contains spiroketals [a confirmed major component: (2S,6R)-(-)(E)-2-methyl-1,7-dioxaspiro[5.5]undecane, and a tentatively identified minor component: 2-ethyl-1,6-dioxaspiro[4.5]decane] and glucose. In this paper, we: 1) illustrate the identification of spiroketals and glucose in the defense spray of A. glaber by using Nuclear Magnetic Resonance (NMR), Gas Chromatography/Mass Spectrometry (GC/MS), and comparison with a synthetic reference sample; 2) provide the elucidation of the absolute configuration of the major spiroketal in that defense spray; and 3) demonstrate the effect of this compound and its enantiomer on both fire ants (Solenopsis invicta) and mosquitoes (Aedes aegypti).

An endogenous bile acid and dietary sucrose from skin secretions of alkaloid-sequestering poison frogs.

The skins of Madagascar poison frogs (Mantella) and certain Neotropical poison frogs (Epipedobates, Dendrobates) secrete the new bile acid tauromantellic acid (1), which was found in both wild-caught and captive-born frogs. This is the first molecule of endogenous origin detected in skin secretions from these taxa. Sucrose was also detected in secretions from wild-caught Mantella but not in captive-born frogs, suggesting a dietary origin.

Hierarchical alignment and full resolution pattern recognition of 2D NMR spectra: application to nematode chemical ecology.

Nuclear magnetic resonance (NMR) is the most widely used nondestructive technique in analytical chemistry. In recent years, it has been applied to metabolic profiling due to its high reproducibility, capacity for relative and absolute quantification, atomic resolution, and ability to detect a broad range of compounds in an untargeted manner. While one-dimensional (1D) (1)H NMR experiments are popular in metabolic profiling due to their simplicity and fast acquisition times, two-dimensional (2D) NMR spectra offer increased spectral resolution as well as atomic correlations, which aid in the assignment of known small molecules and the structural elucidation of novel compounds. Given the small number of statistical analysis methods for 2D NMR spectra, we developed a new approach for the analysis, information recovery, and display of 2D NMR spectral data. We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra. Principle component analysis (PCA) and partial least squares (PLS) regression of full resolution total correlation spectroscopy (TOCSY) spectra greatly aid the assignment and interpretation of statistical pattern recognition results by producing back-scaled loading plots that look like traditional TOCSY spectra but incorporate qualitative and quantitative biological information of the resonances. The HATS-PR methodology is demonstrated here using multiple 2D TOCSY spectra of the exudates from two nematode species: Pristionchus pacificus and Panagrellus redivivus. We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds. These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and biological studies in cellular biochemistry, metabolomics, and chemical ecology.

Alkyldimethylpyrazines in the defensive spray of Phyllium westwoodii: a first for order Phasmatodea.

Phyllium westwoodii is a phasmid insect (Order Phasmatodea) belonging to the Family Phylliidae (leaf insects). These rather large and ornate creatures are known for their morphological resemblance to plant leaves for camouflage. Pyrazines are a common class of compounds used or produced by a wide variety of organisms, even humans. When an individual of P. westwoodii is disturbed, it sprays an opaque liquid from a pair of prothoracic glands, which are utilized by other phasmid species for defense. The current study has found that this liquid contains glucose and a mixture of 3-isobutyl-2,5-dimethylpyrazine, 2,5-dimethyl-3-(2-methylbutyl)pyrazine, and 2,5-dimethyl-3-(3-methylbutyl)pyrazine. This is the first report of pyrazines found in the defensive gland spray of phasmid insects, and the first chemical analysis of glandular material from family Phylliidae.

Bacterial attraction and quorum sensing inhibition in Caenorhabditis elegans exudates.

Caenorhabditis elegans, a bacterivorous nematode, lives in complex rotting fruit, soil, and compost environments, and chemical interactions are required for mating, monitoring population density, recognition of food, avoidance of pathogenic microbes, and other essential ecological functions. Despite being one of the best-studied model organisms in biology, relatively little is known about the signals that C. elegans uses to interact chemically with its environment or as defense. C. elegans exudates were analyzed by using several analytical methods and found to contain 36 common metabolites that include organic acids, amino acids, and sugars, all in relatively high abundance. Furthermore, the concentrations of amino acids in the exudates were dependent on developmental stage. The C. elegans exudates were tested for bacterial chemotaxis using Pseudomonas putida (KT2440), a plant growth promoting rhizobacterium, Pseudomonas aeruginosa (PAO1), a soil bacterium pathogenic to C. elegans, and Escherichia coli (OP50), a non-motile bacterium tested as a control. The C. elegans exudates attracted the two Pseudomonas species, but had no detectable antibacterial activity against P. aeruginosa. To our surprise, the exudates of young adult and adult life stages of C. elegans exudates inhibited quorum sensing in the reporter system based on the LuxR bacterial quorum sensing (QS) system, which regulates bacterial virulence and other factors in Vibrio fischeri. We were able to fractionate the QS inhibition and bacterial chemotaxis activities, thus demonstrating that these activities are chemically distinct. Our results demonstrate that C. elegans can attract its bacterial food and has the potential of partially regulating the virulence of bacterial pathogens by inhibiting specific QS systems.

Relative configuration of natural products using NMR chemical shifts.

We have measured and quantum chemically computed NMR chemical shifts for three monoterpene diastereomers produced by the walkingstick, Anisomorpha buprestoides. By taking into account the Boltzmann distribution of conformers, the combined RMSDs between experimental and calculated (1)H and (13)C NMR shifts were able to determine the correct isomer, especially when only aliphatic nuclei were used. The calculated relative energies and interproton distances were also consistent with chemical isomerization experiments and NOE-based interproton distance calculations. Complementary to the NOE-based method, a comparison between experimental and calculated NMR chemical shifts can provide an efficient method to assign the relative configuration of natural products.

Developmental and geographical variation in the chemical defense of the walkingstick insect Anisomorpha buprestoides.

Anisomorpha buprestoides, a walkingstick common in the southeastern United States, sprays chemicals that irritate and repel threatening insects, birds, or mammals. The active chemical in this substance was initially identified as a monoterpene dialdehyde. This compound can be present in several stereoisomeric forms, and subsequent studies have revealed that A. buprestoides produces at least three diastereomers: anisomorphal, dolichodial, and peruphasmal. However, no inquiry has been made to date into the geographical or developmental dependence of this variation. We report here that different populations of adult A. buprestoides spray either anisomorphal, or peruphasmal, or a mixture of the two stereoisomers. Additionally, offspring of a peruphasmal-producing population produced a variable mixture of anisomorphal and dolichodial but switched to peruphasmal upon reaching sexual maturity. This appears to be the first report of a developmentally regulated change in walkingstick insect chemical defense. Our results suggest a more complex role of these substances in the overall chemical ecology of walkingstick insects.

Strategy for automated analysis of dynamic metabolic mixtures by NMR. Application to an insect venom.

Elucidation of the composition of chemical-biological samples is a main focus of systems biology and metabolomics. Due to the inherent complexity of these mixtures, reliable, efficient, and potentially automatable methods are needed to identify the underlying metabolites and natural products. Because of its rich chemical information content, nuclear magnetic resonance (NMR) spectroscopy has a unique potential for this task. Here we present a generalization and application of a recently introduced NMR data collection, processing, and analysis strategy that circumvents the need for extensive purification and hyphenation prior to analysis. It uses covariance TOCSY NMR spectra measured on a 1-mm high-temperature cryogenic probe that are analyzed by a spectral trace clustering algorithm yielding 1D NMR spectra of the individual components for their unambiguous identification. The method is demonstrated on a metabolic model mixture and is then applied to the unpurified venom mixture of an individual walking stick insect that contains several slowly interconverting and closely related metabolites.

Parectadial, a monoterpenoid from the defensive spray of Parectatosoma mocquerysi.

The defensive secretion of Parectatosoma mocquerysi, a walkingstick insect from Madagascar, was determined to contain glucose, water, and a new monoterpene, parectadial, (4S)-(3-oxoprop-1-en-2-yl)cyclohex-1-enecarbaldehyde. Here, we describe the elucidation of parectadial's molecular structure and absolute configuration via microsample NMR technology, GC-MS, CD, chiral GC-FID, and synthesis from enantiomerically pure (S)- and (R)-perillaldehyde. This work demonstrates the value of walkingstick insects as sources of new bioactive compounds and provides an analytical framework for identifying such substances.

Single insect NMR: A new tool to probe chemical biodiversity.

Because of analytical limitations, multiple animals or plants are typically required to identify natural products. Using a unique 1-mm high-temperature superconducting NMR probe, we directly examined the chemical composition of defensive secretions from walking stick insects. Individual milkings were dissolved in D2O without purification and examined by NMR within 10 min of secretion. We found that Anisomorpha buprestoides secretes similar quantities of glucose and mixtures of monoterpene dialdehydes that are stereoisomers of dolichodial. Different individual animals produce different stereoisomeric mixtures, the ratio of which varies between individual animals raised in the same container and fed the same food. Another walking stick, Peruphasma schultei, also secretes glucose and a single, unique stereoisomer that we are naming "peruphasmal". These observations suggest a previously unrecognized significance of aqueous components in walking stick defensive sprays. Single-insect variability of venom demonstrates the potential importance of chemical biodiversity at the level of individual animals.

NMR analysis of Caenorhabditis elegans FLP-18 neuropeptides: implications for NPR-1 activation.

Phe-Met-Arg-Phe-NH2 (FMRFamide)-like peptides (FLPs) are the largest neuropeptide family in animals, particularly invertebrates. FLPs are characterized by a C-N-terminal gradient of decreasing amino acid conservation. Neuropeptide receptor 1 (NPR-1) is a G-protein coupled receptor (GPCR), which has been shown to be a strong regulator of foraging behavior and aggregation responses in Caenorhabditis elegans. Recently, ligands for NPR-1 were identified as neuropeptides coded by the precursor genes flp-18 and flp-21 in C. elegans. The flp-18 gene encodes eight FLPs including DFDGAMPGVLRF-NH2 and EMPGVLRF-NH2. These peptides exhibit considerably different activities on NPR-1, with the longer one showing a lower potency. We have used nuclear magnetic resonance and biological activity to investigate structural features that may explain these activity differences. Our data demonstrate that long-range electrostatic interactions exist between N-terminal aspartates and the C-terminal penultimate arginine as well as N-terminal hydrogen-bonding interactions that form transient loops within DFDGAMPGVLRF-NH2. We hypothesize that these loops, along with peptide charge, diminish the activity of this peptide on NPR-1 relative to that of EMPGVLRF-NH2. These results provide some insight into the large amino acid diversity in FLPs.