Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae)

Abstract

Certain species within the genus <i>Panax</i> L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as <i>Panax</i>, commonly used DNA barcodes such as nrITS, <i>matK</i>, <i>psbA-trnH</i>, <i>rbcL</i> do not provide species-level resolution. A recent <i>in silico</i> study proposed a set of novel chloroplast markers, <i>trnQ-rps16</i>, <i>trnS-trnG</i>, <i>petB</i>, and <i>trnE-trnT</i> for species level identification within <i>Panax</i>. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of <i>Panax</i>, and two outgroup species of <i>Aralia</i> L. along with empirical data of <i>Panax</i> taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that <i>trnQ-rps16</i> can classify with species level resolution every clade tested here, including the highly valuable <i>Panaxvietnamensis</i> Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within <i>Panax</i> to support both its conservation and commercial trade.