Abstract Detail



Systematics

Ott, Brittany [1], Puente, Caroline [2], Zhang, Ning [1], Greenbaum, Alexandra [1], Windsor, Amanda [3], Wen, Jun [4], Sarmashghi, Shababeddin [5], Arabbaygi, Siavash [6], Bafna, Vineet [7], Timme, Ruth [8], Handy, Sara [9].

The value of Botany in food safety: using phylogenetic tools and genomic data to design innovative detection methods for the allergenic nuts in the genus Carya.

Since 2014, the U.S. Food and Drug Administration (FDA) has been developing a publically available reference library of annotated chloroplast genome sequences and whole genome shotgun raw reads (GenomeTrakrCP, NCBI Bioproject: PRJNA325670). This initiative aims to facilitate traceability and accurate ingredient identification in response to consumer’s demands for more transparency and accountability from the food supply and concerns about labeling and food allergies. The library includes a wide swath of plant groups with a focus on those found in foods and dietary supplements (with a high priority on potential allergen producers), toxin producers, common contaminants, adulterants and their close relatives. These data have facilitated development of simplified assays used to screen food samples for targeted species (e.g., pine nut, peanut and walnut) at FDA-Center for Food Safety and Applied Nutrition.  Through collaborations on this project, here we have collected multiple individuals of 10 species from the genus Carya. This genus includes allergenic nuts such as hickory (C. ovata or C. laciniosa) and pecan (C. illinoinensis). A novel phylogeny was generated using the complete chloroplast genomes. Furthermore, the resulting raw shotgun reads were analyzed using the recently developed program “skmer” to evaluate the ability to identify plant samples from raw whole genome shotgun reads in an effort to simplify identification of unknown food and dietary supplement samples. Finally, the potential utility of the most variable regions of the genome/plastome was examined for future development of targeted assays such as qPCR. This project exemplifies the successful collaboration between academic and non-academic institutions and highlights alternative career paths in which botanical expertise is greatly needed and extremely valuable. 


1 - Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-706, 5001 Campus Dr. , College Park, MD, 20740, USA
2 - U.S. Food And Drug Administration, 5001 Campus Drive, College Park, MD, 20740, United States
3 - Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-706, 5001 Campus Dr, College Park, MD, 20740, USA
4 - Smithsonian Institution, Department Of Botany, P.O. Box 7012, Washington, DC, 20013.0, United States
5 - University of California, San Diego, Electrical and Computer Engineering, San Diego, CA, USA
6 - University of California, Electrical and Computer Engineering, San Diego, CA, USA
7 - University of California, Computer Science and Engineering, San Diego, CA, USA
8 - Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Dr., College Park, MD, 20740, USA
9 - HFS-717, 5001 Campus Dr., College Park, MD, 20740, United States

Keywords:
allergens
DNA based identification
Carya.

Presentation Type: Oral Paper
Number:
Abstract ID:114
Candidate for Awards:None


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