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Systematics, Evolution, and Biodiversity

Member Symposium

Coverage of the Good and the Bad: The Genomes and Genomics of Pollinators and Pests

Chromosome level assembly of a Bacillus thuringiensis resistant strain of the corn earworm, Helicoverpa zea

Tuesday, November 15, 2022

9:55 AM – 10:10 AM PT

Location: Vancouver Convention Centre, Meeting Room 119/120

Presenting Author(s)

BC

Brad S. Coates

Research Geneticist
USDA-ARS
Ames, Iowa

Co-Author(s)

Amanda Stahlke

Computational Biologist
USDA-ARS
Grand Junction, Colorado

Co-author(s)

JC

Jennifer Chang

Iowa state University
Ames, Iowa
Luke R. Tembrock

Research Scientist
Colorado State University
Fort Collins, Colorado
Sheina Biason Sim

Research Biologist
USDA-ARS
Hilo, Hawai'i
SG

Scott M. Geib

Research Entomologist
USDA-ARS
Hilo, Hawai'i
OP

Omaththage Perera

USDA-ARS
Stoneville, Mississippi
Todd M. Gilligan

Biological Scientist
USDA-APHIS
Fort Collins, Colorado

Co-Author(s)

KH

Kevin Hackett

USDA-ARS
Beltsville, Maryland
Anna K. Childers

Computational Biologist
USDA-ARS
Beltsville, Maryland

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 is being used to investigate mechanism(s) of resistance to different Bt transgenic crops.