Fellowship for Kim Vertacnik: Translating Genomics Into Effective Pest Management: Expanding Access To Bioinformatic Resources For Species Identification And Pathway Analysis

Accelerating climate change and globalization are driving unexpected changes in the distribution of invasive pest species. Accurate and rapid species identification and pathway analysis are critical to effective management but oftentimes pests belong to closely related species groups that are morphologically indistinct yet have different ecological impacts. For these, genomic diagnostic marker panels are an important tool for identification. However, genotype calling and analysis relies on bioinformatic pipelines that require a high level of expertise to execute and interpret: a significant barrier to the wide-scale adoption of a powerful phytosanitary resource. To overcome this barrier, this postdoctoral project intends to develop a user-friendly, end-to-end software program for sequence-based diagnostic tool analysis. Starting with next-generation sequencing data, it will flexibly analyze sequence data or call genotypes for probabilistic species identification, down to strain or population depending on the panel, and if applicable, perform geographic source/pathway analysis. Accessibility will be addressed with secure online hosting and the creation of a user-friendly interface. By emphasizing standardization, the software will be intentionally designed as a universal framework for sequencing-based diagnostics, providing flexibility for diverse, taxonomically difficult pest groups. Thus, the proposed work contributes to the AFRI Farm Bill Priority Area: Plant Health and Production and Animal Products and Program Area: 1c. Pests and Beneficial Species in Agricultural Production Systems (Program Area Priority Code: A1112) as a rapid, flexible resource for pest management and fits the AFRI EWD goal of “Advancing Science” by providing training that is highly relevant to the future of the USDA.