Project Number: 2040-22430-026-30-I
Project Type: Interagency Reimbursable Agreement

Start Date: Sep 1, 2017
End Date: Sep 1, 2020

Objective:
Develop diagnostic resources to support identification and eradication of pest fruit flies. In this current agreement, we plan to expand on the prior two year’s Farm Bill project, representing the third year of a multi-year project. In this first two years, we developed and are currently developing genomic resources (whole genome assemblies and annotations) for the melon fly (Bactrocera cucurbitae), Bactrocera correcta, B. zonata and the mexfly (Anastrepha ludens). In addition, utilizing existing specimen repositories for mexfly and medfly, generate genome-wide SNP panels that are being developed as diagnostic population panels. The third year of the project aims to finalize all assemblies and population SNP panels and demonstrate and transfer the technologies to APHIS stakeholders.

Approach:
Develop draft genome references for pest fruit fly species and develop diagnostic assays for source determination of pest flies and species discrimination. Specifically, we are finalizing genome assemblies for B. correcta, B. zonata, B. cucurbitae, and A. ludens. Functional annotation and protein prediction will be performed in addition to attempt chromosome scale scaffolding with long range information if needed. Utilizing these assemblies along with a world-wide collection of wild specimens, a population diagnostic assay for A. ludens, B. cucurbitae, B. correcta and B. zonata will be demonstrated based on genome-wide SNPs. As new specimens are collected from native and invasive populations, these panels will be tested and demonstrated, with the goal of adoption by USDA-APHIS PPQ diagnostic labs.