The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research
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...
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doaj-05011e2bae05449fafe7d043f6f46d352021-07-23T13:47:32ZengMDPI AGInsects2075-44502021-07-011262662610.3390/insects12070626The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod ResearchAnna K. Childers0Scott M. Geib1Sheina B. Sim2Monica F. Poelchau3Brad S. Coates4Tyler J. Simmonds5Erin D. Scully6Timothy P. L. Smith7Christopher P. Childers8Renee L. Corpuz9Kevin Hackett10Brian Scheffler11Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, 10300 Baltimore Avenue, Beltsville, MD 20705, USATropical 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, USATropical 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, USANational Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Avenue, Beltsville, MD 20705, USACorn Insects & Crop Genetics Research Unit, Agricultural Research Service, USDA, 2310 Pammel Dr., Ames, IA 50011, USATropical 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, USAStored Product Insect and Engineering Research Unit, Center for Grain and Animal Health Research, Agricultural Research Service, USDA, 1515 College Avenue, Manhattan, KS 66502, USAGenetics and Breeding Research Unit, U.S. Meat Animal Research Center, Agricultural Research Service, USDA, State Spur 18D, Clay Center, NE 68933, USANational Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Avenue, Beltsville, MD 20705, USATropical 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, USAOffice of National Programs, Crop Production and Protection, Agricultural Research Service, USDA, 5601 Sunnyside Avenue, Beltsville, MD 20705, USAGenomics and Bioinformatics Research Unit, Jamie Whitten Delta States Research Center, Agricultural Research Service, USDA, 141 Experiment Station Road, Stoneville, MS 38776, USAThe 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.https://www.mdpi.com/2075-4450/12/7/626Arthropodapestsinvasive pestsgenome sequencinglong-read sequencinglow-input DNA |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research Insects Arthropoda pests invasive pests genome sequencing long-read sequencing low-input DNA |
author_facet |
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 |
author_sort |
Anna K. Childers |
title |
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research |
title_short |
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research |
title_full |
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research |
title_fullStr |
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research |
title_full_unstemmed |
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research |
title_sort |
usda-ars ag100pest initiative: high-quality genome assemblies for agricultural pest arthropod research |
publisher |
MDPI AG |
series |
Insects |
issn |
2075-4450 |
publishDate |
2021-07-01 |
description |
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. |
topic |
Arthropoda pests invasive pests genome sequencing long-read sequencing low-input DNA |
url |
https://www.mdpi.com/2075-4450/12/7/626 |
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