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. 2017 Mar 16;7(1):216.
doi: 10.1038/s41598-017-00321-6.

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

Ning Zhang  1 , David L Erickson  2 , Padmini Ramachandran  2 , Andrea R Ottesen  2 , Ruth E Timme  2 , Vicki A Funk  3 , Yan Luo  2 , Sara M Handy  2
Affiliations

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

Ning Zhang et al. Sci Rep. .

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.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Gene map of the Echinacea purpurea chloroplast genome. Genes shown outside the circle are transcribed clockwise and those inside are transcribed counterclockwise. Gene belonging to different functional groups are color-coded as indicated by icons on the lower left corner. Dashed area in the inner circle indicates the GC content of the chloroplast genome. LSC, SSC and IR means large single copy, small single copy and inverted repeat, respectively.
Figure 2
Figure 2
The ML tree of Echinacea reconstructed using chloroplast genomes. Numbers on branch nodes are bootstrap values. The branch connecting the outgroup Parthenium argentatum and nine Echinacea species was collapsed.
Figure 3
Figure 3
ML trees reconstructed using matK + rbcL (left) and using chloroplast genomes (right) Numbers are bootstrap values, branches with bootstrap values <50% are collapsed. These two phylogenies show the power of chloroplast genomes for delimitation of Echinacea species when compared with core DNA barcodes.
Figure 4
Figure 4
ML trees reconstructed using ITS (a) and ITS + trnH-psbA (b). Numbers are bootstrap values, branches with the bootstrap value <50% are collapsed. Both phylogenies show the lack of resolution among Echinacea species using either combination of genes.
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