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Article

The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

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Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
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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
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National Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Avenue, Beltsville, MD 20705, USA
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Corn Insects & Crop Genetics Research Unit, Agricultural Research Service, USDA, 2310 Pammel Dr., Ames, IA 50011, USA
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Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, USA
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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
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Genetics and Breeding Research Unit, U.S. Meat Animal Research Center, Agricultural Research Service, USDA, State Spur 18D, Clay Center, NE 68933, USA
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Office of National Programs, Crop Production and Protection, Agricultural Research Service, USDA, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA
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Genomics and Bioinformatics Research Unit, Jamie Whitten Delta States Research Center, Agricultural Research Service, USDA, 141 Experiment Station Road, Stoneville, MS 38776, USA
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Author to whom correspondence should be addressed.
Academic Editor: Alexander Keller
Insects 2021, 12(7), 626; https://doi.org/10.3390/insects12070626
Received: 2 June 2021 / Revised: 20 June 2021 / Accepted: 22 June 2021 / Published: 9 July 2021
(This article belongs to the Special Issue Insect Genomics)
High-quality genome assemblies are essential tools for modern biological research. In the past, creating genome assemblies was prohibitively expensive and time-consuming for most non-model insect species due to, in part, the technical challenge of isolating the necessary quantity and quality of DNA from many species. Sequencing methods have now improved such that many insect genomes can be sequenced and assembled at scale. We created the Ag100Pest Initiative to propel agricultural research forward by assembling reference-quality genomes of important arthropod pest species. Here, we describe the Ag100Pest Initiative’s processes and experimental procedures. We show that the Ag100Pest Initiative will greatly expand the diversity of publicly available arthropod genome assemblies. We also demonstrate the high quality of preliminary contig assemblies. We share arthropod-specific technical details and insights that we have gained during the project. The methods and preliminary results presented herein should help other researchers attain similarly high-quality assemblies, effectively changing the landscape of insect genomics.
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. View Full-Text
Keywords: Arthropoda; pests; invasive pests; genome sequencing; long-read sequencing; low-input DNA; HiC scaffolding; genome assembly; genomics Arthropoda; pests; invasive pests; genome sequencing; long-read sequencing; low-input DNA; HiC scaffolding; genome assembly; genomics
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MDPI and ACS Style

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.; Hackett, K.; Scheffler, B. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects 2021, 12, 626. https://doi.org/10.3390/insects12070626

AMA Style

Childers AK, Geib SM, Sim SB, Poelchau MF, Coates BS, Simmonds TJ, Scully ED, Smith TPL, Childers CP, Corpuz RL, Hackett K, Scheffler B. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects. 2021; 12(7):626. https://doi.org/10.3390/insects12070626

Chicago/Turabian Style

Childers, Anna K., 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, and Brian Scheffler. 2021. "The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research" Insects 12, no. 7: 626. https://doi.org/10.3390/insects12070626

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