BackgroundThe economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination.ResultsWe used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus.ConclusionsMBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1160-y) contains supplementary material, which is available to authorized users.

11Background 12The economic value of ginseng in the global medicinal plant trade is estimated to be in excess 13 of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) 14 and the complex evolutionary history of the genus is poorly understood despite several 15 molecular phylogenetic studies. In this study, we use a full plastome phylogenomic 16 framework to resolve relationships in Panax and to identify molecular markers for species 17 discrimination. 18 Results 19We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement 20 publicly available plastid genomes to create a phylogeny based on fully assembled and 21 annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on 22 a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The 23 closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome 24 matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for 25 unambiguous molecular identification of all the represented species in the genus. 26 Conclusions 27MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective 28 alternative to Sanger sequencing based DNA barcoding for molecular identification. The 29 plastome phylogeny provides a robust framework that can be used to study the evolution of 30 morphological characters and biosynthesis pathways of ginsengosides for phylogenetic 31 bioprospecting. Molecular identification of ginseng species is essential for authenticating 32 ginseng in international trade and it provides an incentive for manufacturers to create 33 authentic products with verified ingredients. 34 35 3 Plastid 37 38 39 Background 40 41Ginseng has been used in traditional medicine in China for thousands of years [1], but 42 it was not until early 18th century that long-term, intense harvest nearly extirpated Panax 43 ginseng C.A.Mey. from the wild [2]. Demand for ginseng roots in the 18th century also 44 fuelled a subsequent boom in wild-harvesting American ginseng (P. quinquefolius L.) that 45 decimated wild populations in North America [3]. Today wild P. ginseng occurs in only a few 46 localities in Russia and China, with the largest distribution in the southern part of the Sikhote-47 Alin mountain range [4]. P. ginseng is Red-Listed in Russia, and roots and parts thereof from 48Russian populations are CITES Appendix II/NC listed [5]. Many other Asian ginseng species 49 are also endangered but preliminary data is only available for wild-harvesting and 50 conservation of P. assamicus R.N.Banerjee (synonym of P. bipinnatifidus var. angustifolius 51 (Burkill) J.Wen) [6], P. japonicus (T.Nees) C.A.Mey. [7] and P. pseudoginseng Wall. [8, 9]. 52Elucidating the evolutionary relationships among species in the genus is essential to 53 understand evolution of this Holarctic disjunct genus, but also evolution of derived secondary 54 metabolite pathways. In addition, a phylogenetic framework can...

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