Genome and Genetic Engineering of the House Cricket (Acheta domesticus) Applications for Sustainable Agriculture

Dossey, A. T.; Oppert, B.; Chu, F.-C.; Lorenzen, M. D.; Scheffler, B.; Simpson, S.; Koren, S.; Johnston, J. S.; Kataoka, K.; Ide, K.

doi:10.1101/2022.12.14.520443

bioRxiv · 10.1101/2022.12.14.520443

Genome and Genetic Engineering of the House Cricket (Acheta domesticus) Applications for Sustainable Agriculture

Dossey, A. T.·Oppert, B.·Chu, F.-C.·Lorenzen, M. D.·Scheffler, B.·Simpson, S.·Koren, S.·Johnston, J. S.·Kataoka, K.·Ide, K.

View original source ↗Export metadata ↓

Abstract

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 StatementSequencing and assembly of the genome of the house cricket has led to improvements in farmed insects for food, pharmaceutical and other applications.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Dossey, A. T., Oppert, B., Chu, F.-C., Lorenzen, M. D., Scheffler, B., Simpson, S., Koren, S., Johnston, J. S., Kataoka, K., Ide, K.. 2022-12-16. Genome and Genetic Engineering of the House Cricket (Acheta domesticus) Applications for Sustainable Agriculture. https://doi.org/10.1101/2022.12.14.520443

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗

bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗

bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗