The USDA-ARS Ag100pest initiative: High-quality Genome Assemblies for Agricultural Pest Arthropod Research

Authors

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

ORCID IDs

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

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

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

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

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

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

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

Date of this Version

7-1-2021

Document Type

Article

Citation

Insects (2021) 12: 626

doi: 10.3390/ insects12070626

Comments

United States government work

Also licensed Creative Commons Attribution (CC BY)

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.