The USDA-ARS Ag100pest initiative: High-quality genome assemblies for agricultural pest arthropod research

Authors

Anna K. Childers, USDA ARS Beltsville Agricultural Research CenterFollow
Scott M. Geib, USDA Agricultural Research ServiceFollow
Sheina B. Sim, USDA Agricultural Research ServiceFollow
Monica F. Poelchau, USDA ARS Beltsville Agricultural Research CenterFollow
Brad S. Coates, USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IAFollow
Tyler J. Simmonds, USDA Agricultural Research ServiceFollow
Erin D. Scully, USDA Agricultural Research ServiceFollow
Timothy P.L. Smith, USDA ARS Roman L. Hruska U.S. Meat Animal Research CenterFollow
Christopher P. Childers, USDA ARS Beltsville Agricultural Research CenterFollow
Renee L. Corpuz, USDA Agricultural Research ServiceFollow
Kevin Hackett, USDA ARS Beltsville Agricultural Research CenterFollow
Brian Scheffler, USDA Agricultural Research Service, StonevilleFollow

ORCID IDs

Anna K. Childers https://orcid.org/0000-0002-0747-8539

Scott M. Geib https://orcid.org/0000-0002-9511-5139

Sheina B. Sim https://orcid.org/0000-0003-0914-6914

Monica F. Poelchau https://orcid.org/0000-0002-4584-6056

Erin D. Scully https://orcid.org/0000-0002-8315-5619

Timothy P. L. Smith https://orcid.org/0000-0003-1611-6828

Christopher P. Childers https://orcid.org/0000-0002-1253-5550

Date of this Version

7-1-2021

Document Type

Article

Citation

Childers, A.K.; Geib, S.M.; Sim, S.B.; Poelchau, M.F.; Coates, B.S.; Simmonds, T.J.; Scully, E.D.; Smith, T.P.L.; Childers, C.P.; Corpuz, R.L.; et al. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects 2021, 12, 626. https://doi.org/10.3390/ insects12070626

Comments

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license

Abstract

The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale.