Insect Genome Assemblies Advanced by Early Adoption of Dovetail Technologies

Dr. Brenda Oppert, PhD, USDA-ARS

Agriculture is facing a number of challenges to sustain expanding populations worldwide. Climate change is contributing to decreased water and land resources for agriculture, as well as shifting pest populations. Our research interfaces at two points in the food chain. For years our research has focused on protecting grains and grain products from stored product insects at the end of the chain. Initially, we developed genomic resources for some of the more problematic stored product insects. However, with the increasing need to identify new sustainable protein sources, we transitioned to developing genomic resources for insects as food. Insects can provide a valuable source of protein and require much less water and land per pound of protein compared to other animals. As the number of insect farms are expanding worldwide, genetic tools are needed to improve insect traits for feed applications. I will detail our six reference insect genome assemblies. We developed a procedure to obtain high quality long genomic DNA that has been successfully sequenced on PacBio platforms (RSII, Sequel I and II). Draft assemblies were scaffolded with Chicago and Hi-C libraries in HiRise. In some species, we obtained transcriptome resources to improve annotation and examine differential gene expression among the different life stages and sexes. Most recently, we are using Dovetail’s annotation pipeline to accelerate the release of reference quality genome assemblies. I will provide examples of how the data from genome and transcriptome assemblies are being used in genetic transformation to solve problems related to storage pests and farmed insects.