Beneficial insects including bee pollinators are vital for agricultural and ecosystem function. Conversely, arthropod pests negatively impact field crops, livestock, trees, bees, and stored products. We will provide a high-level overview of multi-institutional efforts to generate reference genome resources for both pests and pollinators. The Beenome100 Project is led by the USDA’s Agricultural Research Service (USDA-ARS) and the University of Illinois. This project leverages unique expertise in insect genomics and pollinator research from both institutions and from a growing cadre of experts in bees, pollination, bioinformatics, and ‘omics of all types. The Ag100Pest Initiative is a USDA-ARS effort to produce annotated, reference quality genome assemblies for the top 100 US arthropod agricultural pests by leveraging unique expertise in arthropod pest management and genomics research. We are pushing the limits of current technology to produce long-read sequencing data from individual specimens, despite the challenges of small body sizes, and sometimes large genomes, presented by arthropods. Current efforts have led to dozens of genome assemblies for both pest and pollinator species and project resources are being made available via NCBI’s Genbank and other database and analytical homes. Simultaneously, topical experts are carrying out comparative studies from neurobiology and metagenomics to resistance and adaptation. These efforts support the goals of umbrella international genome sequencing efforts including the i5K initiative (http://i5k.github.io/) and the Earth BioGenome Project (https://www.earthbiogenome.org/). This talk will highlight progress and opportunities in both efforts along with insights into best practices from process and data management to extraction, sequencing, assembly, and annotation.
