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

Certain species within the genus Panax 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 Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. 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 Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panaxvietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.

Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or dioxin, is commonly considered the most toxic man-made substance. Dioxin exposure impacts human health and diseases, birth defects and teratogenesis were frequently observed in children of persons who have been exposed to dioxin. However, the impact of dioxin on human mutation rate in trios has not yet been elucidated at the whole genome level. To identify and characterize the genetic alterations in the individuals exposed to dioxin, we performed whole genome sequencing (WGS) of nine Vietnamese trios whose fathers were exposed to dioxin. In total, 846 de novo point mutations, 26 de novo insertions and deletions, 4 de novo structural variations, and 1 de novo copy number variation were identified. The number of point mutations and dioxin concentrations were positively correlated (P-value < 0.05). Considering the substitution pattern, the number of A > T/T > A mutation and the dioxin concentration was positively correlated (P-value < 0.05). Our analysis also identified one possible disease-related mutation in LAMA5 in one trio. These findings suggested that dioxin exposure might affect father genomes of trios leading to de novo mutations in their children. Further analysis with larger sample sizes would be required to better clarify mutation rates and substitution patterns in trios caused by dioxin.

Isolation and characterization of the 4-coumarate:coenzyme A ligase (4CL1) promoter from Eucalyptus camaldulensis.

The most important enzyme of the phenylpropanoid pathway, 4-coumarate:coenzyme A ligase (4CL), is encoded by several homologous genes including 4CL1. The 4CL1 promoter is a tissue-specific gene expression element, particularly active in the secondary xylem or older stems. In this study, the 1127 bp 5'- upstream region of the 4CL1 coding sequence from Eucalyptus camaldulensis, Euc4CL1, was isolated and characterized. Essential putative cis-elements in the Euc4CL1 promoter included: a TATA-box at -22/-28 position, two CCAAT-boxes at -256/-260 and -277/-281 positions, respectively, an AC-element at -328/-336 and A-boxes at -115/-120 and -990/-995 positions. To investigate the effect of the Euc4CL1 promoter on gene expression, a plant transformation vector, pEuc4CL1p, containing the reporter gene for ß-glucuronidase (GUS) under the control of Euc4CL1 promoter was constructed based on the pBI101 backbone and introduced in tobacco plants. Stable expression of the GUS gene in transgenic lines was analysed by a histochemical GUS assay. The results indicated the specific expression of the GUS gene in the stem xylem cells of transgenic tobacco lines was controlled by the Euc4CL1 promoter. The observations suggest the isolated Euc4CL1 promoter is a potential candidate for driving the expression of a foreign gene in plant xylem tissues.