Implementing low-cost, high accuracy DNA barcoding from single molecule sequencing to screen larval tephritid fruit fly intercepted at ports of entry

Authors: GARZON, IVONNE - University Of Hawaii; Geib, Scott; BREMER, FOREST - University Of Hawaii; BARR, NORMAN - Animal And Plant Health Inspection Service (APHIS)

Submitted to: Annals of the Entomological Society of America
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/4/2019
Publication Date: 3/16/2020
Citation: Garzon, I., Geib, S.M., Bremer, F., Barr, N. 2020. Implementing low-cost, high accuracy DNA barcoding from single molecule sequencing to screen larval tephritid fruit fly intercepted at ports of entry. Annals of the Entomological Society of America. 113(4):288-297. https://doi.org/10.1093/aesa/saz071.
DOI: https://doi.org/10.1093/aesa/saz071

Interpretive Summary: Recurrently invading pests are those which are not established in a given area but intercepted frequently and prevented from establishing through control efforts. Tephritid fruit flies are such recurrently invading pests in the continental USA, and when these flies are intercepted in regular monitoring efforts one of the main questions is “where did they come from?”. Here, we use population genomics to create a diagnostic tool for the Mexican fruit fly, Anastrepha ludens, which is native to Mexico & Central America and often intercepted in Texas and California. By using >2 thousand genome-wide markers, we assess population structure across this species’ range, and identify found main population clusters. We then identify 28 highly informative markers from the genome-wide dataset, which can accurately recreate the population structure found when using >2 thousand markers. We use this panel to predict the source for a set of real-world test specimens, many of which were intercepted in regular monitoring efforts in Texas and California. This approach provides a applied genomic framework for creating such a diagnostic tool for source determination of recurrently invading pests, and is the first demonstration of such an approach on intercepted specimens in an agricultural pest system.

Technical Abstract: Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction-site associated DNA sequencing, and then developed and demonstrated a panel of highly-differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genome-wide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly-differentiated SNPs that were able to recreate the genome-wide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.