title: An analysis of Echinacea chloroplast genomes: Implications for future botanical identification.
abstract: Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field. We used Next Generation Sequencing (NGS) and CLC Genomics Workbench to assemble complete chloroplast genomes for all nine species. Full chloroplasts unambiguously differentiated all nine species, compared with the very few single nucleotide polymorphisms (SNPs) available with core DNA barcoding markers. SNPs for any two Echinacea chloroplast genomes ranged from 181 to 910, and provided robust data for unambiguous species delimitation. Implications for DNA-based species identification assays derived from chloroplast genome sequences are discussed in light of product safety, adulteration and quality issues.
authors.affiliation: Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States. ning.zhang@fda.hhs.gov.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
authors.forename: David L
authors.initials: DL
authors.lastname: Erickson
authors.affiliation: Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
authors.forename: Padmini
authors.initials: P
authors.lastname: Ramachandran
authors.affiliation: Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
authors.forename: Andrea R
authors.initials: AR
authors.lastname: Ottesen
authors.affiliation: Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
authors.forename: Ruth E
authors.initials: RE
authors.lastname: Timme
authors.affiliation: Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-0166, USA.
authors.forename: Vicki A
authors.initials: VA
authors.lastname: Funk
authors.affiliation: Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
authors.forename: Yan
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
authors.forename: Sara M
authors.initials: SM
authors.lastname: Handy
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic; D018742:DNA, Chloroplast / Q000032:analysis; D018744:DNA, Plant / Q000032:analysis; D020900:Echinacea / Q000145:classification* / Q000166:cytology / Q000235:genetics; D054628:Genome, Chloroplast; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant