Skip to main content
ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » ABADRU » Research » Publications at this Location » Publication #411287
Research Project: Biology and Management of Dipteran Pests of Livestock and Other Animals

Location: Arthropod-borne Animal Diseases Research

Title: otb: an Automated HiC/HiFi Pipeline Assembles the Prosapia bicincta Genome

Author
item Molik, David
item STAHLKE, AMANDA - Colorado Mesa University
item SHARMA, SHARU - Iowa State University
item Corpuz, Renee
item Kauwe, Angela
item Schrader, Jeremy
item Mason, Charles
item Sim, Sheina
item Geib, Scott

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2024
Publication Date: 6/11/2024
Citation: Molik, D.C., Stahlke, A., Sharma, S.P., Corpuz, R.L., Kauwe, A.N., Schrader, J.E., Mason, C.J., Sim, S.B., Geib, S.M. 2024. otb: an Automated HiC/HiFi Pipeline Assembles the Prosapia bicincta Genome. Genes, Genomes, and Genomics. 14(7). https://doi.org/10.1093/g3journal/jkae129.
DOI: https://doi.org/10.1093/g3journal/jkae129

Interpretive Summary: In this paper we present a Genome Assembly of the two-lined spittlebug, an herbivorous insect native to tropical and subtropical regions globally and widely spread across the eastern United States that has major impacts on grassland landscapes. The two-lined spittlebug feeds on turf grasses and pasturelands which leads to wilting and phytotoxemia, ultimately causing plants to die. By altering plant communities in rangelands, this also pest also poses a substantial threat to cattle production due to loss of rangeland and pastures. ARS has been studying this insect's genetics to gain a deeper understanding of its physiology, ecology, and evolution. Utilizing phased genomes, a cutting-edge approach in genomics, the team aimed to identify new targets for sustainable pest management. This paper presents an advancement; a HiC/HiFi phased genomics assembly pipeline named Only The Best (otb). This innovative pipeline has successfully addressed several challenges related to data management that were previously encountered during the creation and storage of genome assemblies. These advancements can potentially revolutionize pest management strategies and protect agricultural landscapes from the detrimental impacts of the two-lined spittlebug.

Technical Abstract: The implementation of a new genomic assembly pipeline named Only The Best (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The primary objective of otb is to streamline the process of creating a HiFi/HiC genome, aiming to minimize the manual intervention required in the genome assembly process. The Two-lined spittlebug, Prosapia bicincta, Hemiptera: Cercopidae), a true bug insect herbivore, serves as a practical test case for evaluating otb. The two-lined spittlebug is both a crucial agricultural pest and a genomically understudied insect belonging to the order Hemiptera. 6This insect is a significant threat to grasslands and pastures, leading to plant wilting and phytotoxemia when infested. Its presence in tropical and subtropical regions around the world poses a long-term threat to the composition of plant communities in grassland landscapes, impacting rangelands, and posing a substantial risk to cattle production.