Panax plastid genome matrix

Full plastid alignment of 61 Araliaceae plastid genomes. Plastome phylogenomics resolves relationships in Panax and identifies markers for molecular identificationManzanilla V.1, Kool A. 1, Nguyen Nhat L. 2, Nong Van H. 2, Le Thi Thu H.2§, de Boer H.J.1§1. The Natural History Museum, University of Oslo, Oslo, Norway2. Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam§ These authors are co-last authors.AbstractThe 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 among Panax genus and to identify molecular markers for species discrimination. We 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 is based on a 163 kbp matrix and resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species, P. vietnamensis, described in 1985, is supported as the 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. MBD2 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 provides an incentive for manufacturers to create authentic products with verified ingredients.