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

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.

Keywords: Arthropoda; HiC scaffolding; genome assembly; genome sequencing; genomics; invasive pests; long-read sequencing; low-input DNA; pests.

Figure 1

Workflow used by Ag100Pest to generate annotated reference-quality assemblies.

Figure 2

Venn diagrams showing the number of species present in NCBI for the phylum Arthropoda at the initiation of the Ag100Pest Initiative and at present compared to the species included in the Ag100Pest Initiative. NCBI data was accessed on 24 October 2018 and 27 April 2021, respectively. The top row includes all species present in NCBI, and the bottom row includes only those species with an assembly deemed high-quality at the taxonomic levels of order, family, and species. Assemblies with a contig N50 of 1 Mbp or greater and scaffolding with an N50 of 10 Mbp or greater were deemed high-quality. Assemblies without clear scaffolding (scaffold N50 > contig N50) were not evaluated as high-quality. We strive to produce high-quality genome assemblies for all species covered by the Ag100Pest Initiative.

Figure 3

Plot of contig N50 (Mbp) versus genome size (Mbp) for Ag100Pest assemblies. This data was gathered from 47 insect genomes that have completed HiFi sequencing and were assembled by the Ag100Pest Initiative. Assemblies that require additional sequencing to achieve a high-quality assembly were excluded from the dataset. The data was plotted on a logarithmic axis to reduce skew from outliers, and data points were color-coded based on order.