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

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

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 4/12/2022
Publication Date: 4/12/2022
Citation: Stahlke, A.R., Chen, J.M., 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 Bacillus thuringiensis Cry1Ac insecticidal protein resistant strain of Helicoverpa zea. bioRxiv. 1-23. https://doi.org/10.1101/2022.04.12.488070.
DOI: https://doi.org/10.1101/2022.04.12.488070

Interpretive Summary: Caterpillars that feed on corn ears or cotton bolls cause reductions in crop yield, product quality, and farmer profit. Crop damage caused by the corn earworm (CEW; also known as the cotton bollworm) can be controlled by use of transgenic crops that express Bacillus thuringiensis (Bt) pesticidal proteins and applications of chemical insecticides. CEW resistance to several Bt crops and insecticides has become more common, which leaves growers fewer options to control crop damage. The lack of genomic resources for CEW hinders research into resistance mechanisms and sustainability of current control tactics. ARS scientists and university collaborators generated a genome assembly for a Bt resistant laboratory strain of CEW. This high-quality assembly is composed of intact chromosomes and a complete set of predicted genes, and is a tool for future research on Bt and insecticide resistance. This work will be of interest to stakeholders including government, university, and industry researchers as well as regulatory agencies concerned about the impacts of insecticide resistance on 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 has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. H. zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological 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 were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single-copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.