An analysis of Echinacea chloroplast genomes: Implications for future botanical identification

Ning Zhang,Padmini Ramachandran,Sara M. Handy,Yan Luo,Ruth E. Timme,Vicki A. Funk,Andrea R. Ottesen,David L. Erickson

doi:10.1038/s41598-017-00321-6

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.

Highlights

Echinacea, i.e., purple coneflower, is one of the most popular botanicals used in dietary supplements
Even when Echinacea species are being used in products, it is not easy to differentiate among the three most appropriate Echinacea species, i.e., E. purpurea, E. angustifolia, and E. pallida; as a result, mislabeling occurs frequently[15, 16]
The data gathered for each species ranged from 434 MB for E. tennessensis to 2,531 MB for E. purpurea, with coverage of chloroplast genomes ranging between 20x for E. tennessensis and 65x for E. angustifolia

Summary

Introduction

I.e., purple coneflower, is one of the most popular botanicals used in dietary supplements. The range of Echinacea spans the Atlantic drainage region of the United States and extends into south central Canada[1] For this genus, the Southern United Stated is an important native area with two species, i.e. E_tennesseensis and E. laevigata endemic to the southeast United States. Ardjommand-woelkart and Bauer (2016), among others, have noted that both E. angustifolia (whole plant) and E. purpurea (dry root) have been associated with allergic reactions[11,12,13] Aside from these few instances, there are no known drug interactions or side effects[8] associated with the 9 species. Distinguishing among Echinacea species using molecular methods is challenging due to extremely low levels of molecular divergence This reflects a pattern seen among other members of Asteraceae, which demonstrate substantial morphological variation, but very little molecular differentiation, due to recent and rapid species radiations[17, 18]. Flagel et al.[19] used three nuclear markers (Adh, CesA, and GPAT) and two plastid loci (trnS and trnG) to examine the phylogeny of Echinacea; no resolved topologies were obtained, suggesting incomplete lineage sorting, as well as the potential for widespread hybridization within the genus[19]

Methods

Results

Conclusion