Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton

Authors: Stahlke, Amanda; CHANG, JENNIFER - Oak Ridge Institute For Science And Education (ORISE); CHUDALAYANDI, SIVANANDAN - Iowa State University; HEU, CHAN - Oak Ridge Institute For Science And Education (ORISE); Geib, Scott; Scheffler, Brian; Childers, Anna; Fabrick, Jeffrey

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2023
Publication Date: 2/15/2023
Citation: Stahlke, A.R., Chang, J., Chudalayandi, S., Heu, C.C., Geib, S.M., Scheffler, B.E., Childers, A.K., Fabrick, J.A. 2023. Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton. G3, Genes/Genomes/Genetics. 13(4). Article jkad040. https://doi.org/10.1093/g3journal/jkad040.
DOI: https://doi.org/10.1093/g3journal/jkad040

Interpretive Summary: The pink bollworm, Pectinophora gossypiella, is one of the world's most important pests of cotton. Field management currently relies on chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). A combination of these strategies contributed to the eradication of pink bollworm from the cotton growing areas of the United States and northern Mexico. However, pink bollworm remains a major pest of in other parts of world and in Asia the benefits of using Bt cotton has been lost due to resistance evolution. Although the pink bollworm is useful as a practical model for understanding resistance to Bt toxins, advances in understanding at the molecular level have been limited due to the absence of basic genomic information for this cosmopolitan pest. Here, ARS scientists from Maricopa, AZ, Beltsville, MD, Stoneville, MS, and Hilo, HI, and their collaborators generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S). The fully annotated genome exceeds established quality standards, has a low error-rate, is highly contiguous, and is complete. The genome consists of 14,107 protein-coding genes representing more than 41,000 functional annotations. This assembly represents the first publicly available complete, annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.

Technical Abstract: The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), is a major global pest of cotton. Current management practices include chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). These strategies have contributed to eradication of P. gossypiella from the cotton growing areas of the United States and northern Mexico. However, this pest has evolved resistance to Bt cotton in Asia, where it remains a critical pest, and the benefits of using transgenic Bt crops have been lost. A complete annotated reference genome is needed to improve global Bt resistance management of the pink bollworm. We generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S) using PacBio continuous long reads for contig generation, Illumina Hi-C for scaffolding, and Illumina whole-genome re-sequencing for error-correction. The psuedohaploid assembly consists of 29 autosomes and the Z sex chromosome. The assembly exceeds the minimum Earth BioGenome Project quality standards, has a low error-rate, is highly contiguous at both the contig and scaffold level (L/N50 of 18/8.26 MB and 14/16.44 MB, respectively), and complete, with 98.6% of lepidopteran single-copy orthologs represented without duplication. The genome was annotated with 50% repeat content and 14,107 protein-coding genes, further assigned to 41,666 functional annotations. This assembly represents the first publicly available complete annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.