The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research
Anna K. Childers,
Scott M. Geib,
Sheina B. Sim,
Monica F. Poelchau,
Brad S. Coates,
Tyler J. Simmonds,
Erin D. Scully,
Timothy P. L. Smith,
Christopher P. Childers,
Renee L. Corpuz,
Kevin Hackett,
Brian Scheffler
Affiliations
Anna K. Childers
Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
Scott M. Geib
Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, USDA, 64 Nowelo Street, Hilo, HI 96720, USA
Sheina B. Sim
Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, USDA, 64 Nowelo Street, Hilo, HI 96720, USA
Monica F. Poelchau
National Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Avenue, Beltsville, MD 20705, USA
Brad S. Coates
Corn Insects & Crop Genetics Research Unit, Agricultural Research Service, USDA, 2310 Pammel Dr., Ames, IA 50011, USA
Tyler J. Simmonds
Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, USDA, 64 Nowelo Street, Hilo, HI 96720, USA
Erin D. Scully
Stored Product Insect and Engineering Research Unit, Center for Grain and Animal Health Research, Agricultural Research Service, USDA, 1515 College Avenue, Manhattan, KS 66502, USA
Timothy P. L. Smith
Genetics and Breeding Research Unit, U.S. Meat Animal Research Center, Agricultural Research Service, USDA, State Spur 18D, Clay Center, NE 68933, USA
Christopher P. Childers
National Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Avenue, Beltsville, MD 20705, USA
Renee L. Corpuz
Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, USDA, 64 Nowelo Street, Hilo, HI 96720, USA
Kevin Hackett
Office of National Programs, Crop Production and Protection, Agricultural Research Service, USDA, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA
Brian Scheffler
Genomics and Bioinformatics Research Unit, Jamie Whitten Delta States Research Center, Agricultural Research Service, USDA, 141 Experiment Station Road, Stoneville, MS 38776, USA
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.
