Using novel, low-cost sequencing technologies to increase genomic resources for agricultural pests

Global shipping and trade practices greatly facilitate the introduction of insect pests into new host ranges. Once established, these invaders can have detrimental impacts on local ecosystems, agricultural production, and... [ view full abstract ]

Global shipping and trade practices greatly facilitate the introduction of insect pests into new host ranges. Once established, these invaders can have detrimental impacts on local ecosystems, agricultural production, and even food processing/storage facilities, which can provide optimal sources of nutrition and environmental conditions that enable rapid population growth. Often times, not much is known about the biology of these introduced pests, but it is essential to devise rapid and effective control measures to eliminate and prevent them from spreading beyond the initial site of introduction.  Recent insect genome sequencing efforts have greatly expanded our understanding of the metabolic and physiology capacities of emerging invasive pests and have also lead to the identification of genetic factors that contribute to host range, tolerance to biotic stresses, and resistance to various insecticides, all of which can greatly expedite management decisions.   However, the inability to obtain sufficient concentrations of high-quality DNA has impeded the rapid development of genome assemblies for many economically devastating agricultural pests.  Using 10X Chromium libraries, we have obtained high quality draft assemblies of three major aphid pests of bioenergy grasses (yellow sugar cane aphid, sugar cane aphid, and greenbug) with total assembly lengths that exceeded 90% of the estimated genome sizes and had contig N50s>100kb and scaffold N50s>2 Mb.  The DNA libraries were created from pools of multiple clonal individuals, demonstrating that high quality de novo genome assemblies can be created for aphids using10X Chromium libraries.  In addition, we are also applying these library and assembly techniques to stored product pests belonging to six different insect families.  In these cases, DNA isolated from single individuals was used to prepare Chromium libraries in order to circumvent inbreeding, which can be time consuming and difficult for certain insect species, and pooling multiple individuals, which can cause assembly breaks due to allelic differences between individuals and heterozygosity.  The 10X assemblies will ultimately be coupled with high density linkage maps and Oxford Nanopore sequencing to generate higher order scaffolds.  Once completed, these genomes will provide us with platforms to study the genetic mechanisms of pesticide resistance, tolerance to stresses, and ability to perceive and respond to food odors in a variety of different insect pests. Ultimately, this information will greatly facilitate management decisions for control for invasive pests.