Planta Med
DOI: 10.1055/s-0043-113449
Original Papers
Georg Thieme Verlag KG Stuttgart · New York

Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP

Ning Zhang1, Padmini Ramachandran1, Jun Wen2, James A. Duke3, Helen Metzman3, William McLaughlin4, Andrea R. Ottesen1, Ruth E. Timme1, Sara M. Handy1
  • 1Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
  • 2Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington D. C., United States
  • 3Green Farmacy Garden, Fulton, Maryland, United States
  • 4United States Botanic Garden Conservatory, Washington D. C., United States
Further Information

Publication History

received 07 March 2017
revised 21 May 2017

accepted 05 June 2017

Publication Date:
26 June 2017 (eFirst)

Abstract

Precise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences. Here, we introduce a repository of complete chloroplast genome sequences called GenomeTrakrCP, which will be publicly available at the National Center for Biotechnology Information (NCBI). Target species for inclusion are plants found in foods and dietary supplements, toxin producers, common contaminants and adulterants, and their close relatives. Publicly available data will include annotated assemblies, raw sequencing data, and voucher information with each NCBI accession associated with an authenticated reference herbarium specimen. To date, 40 complete chloroplast genomes have been deposited in GenomeTrakrCP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA325670/), and this will be expanded in the future.