A chromosome-scale genome assembly of a Helicoverpa zea strain resistant to Bacillus thuringiensis Cry1Ac insecticidal protein

Authors: Stahlke, Amanda; CHEN, JENNIFER - Iowa State University; TEMBROCK, LUKE - Animal And Plant Health Inspection Service (APHIS); Sim, Sheina; CHUDALAYANDI, SIVA - Iowa State University; Geib, Scott; Scheffler, Brian; Perera, Omaththage; GILLIGAN, TODD - Colorado State University; Childers, Anna; Hackett, Kevin; Coates, Brad

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2022
Publication Date: 8/12/2022
Citation: Stahlke, A.R., Chen, J., Tembrock, L.R., Sim, S.B., Chudalayandi, S., Geib, S.M., Scheffler, B.E., Perera, O.P., Gilligan, T.M., Childers, A.K., Hackett, K.J., Coates, B.S. 2022. A chromosome-scale genome assembly of a Helicoverpa zea strain resistant to Bacillus thuringiensis Cry1Ac insecticidal protein. Genome Biology and Evolution. 15(3). Article evac131. https://doi.org/10.1093/gbe/evac131.
DOI: https://doi.org/10.1093/gbe/evac131

Interpretive Summary: Insects that feed on corn ears or cotton bolls reduce crop yields, product quality, and farmer profits. Damage caused by the corn earworm (CEW; also known as the cotton bollworm) can be reduced by planting transgenic crops that express Bacillus thuringiensis (Bt) pesticidal proteins and application of chemical insecticides. CEW has developed resistance to several Bt crops and insecticides, which leaves growers fewer option to control crop damage. Research on resistance mechanisms has been hindered by the lack of genomic resources for CEW. Using novel methods developed by a team of ARS scientists from the Ag100Pest Initiative and university collaborators, a high-quality genome assembly was generated for a Bt resistant strain of CEW. This CEW genome assembly is composed of intact chromosomes and a comprehensive set of predicted genes. The assembly is a valuable resource for investigating changes in the CEW genome that can be associated with resistance to Bt crops and insecticides. This work will be of interest to government, university, and industry researchers as well as stakeholders in corn and cotton commodity groups and regulatory agencies concerned about the development of insecticide resistant populations and the sustainability of insect control strategies.

Technical Abstract: Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species is highly adaptable to different host plants and has developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Populations of H. zea persist in tropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. In order to facilitate understanding of these biological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt resistant strain, HzStark_Cry1AcR. Hi-C data scaffolded an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 13.0 Mb and L50 = 14). The genome is composed of approximately 29% repetitive and transposable elements. Assessment with the Lepidopteran Benchmark Universal Single-Copy Ortholog set indicated 98.8% were complete and 98.5% complete single-copy. This chromosome-scale reference assembly for H. zea will future research to evaluate and enhance sustainable crop production practices.