Genomic tools for identification of medicinal plants

DNA barcoding of herbal medicines has raised awareness of species substitution and adulteration, highlighting issues surrounding their safety and quality. Regulation of herbal medicines is a pressing issue for regulatory agencies and, in response, DNA barcodes have recently been incorporated into the British Pharmacopoeia. Previous studies have found that DNA barcoding to species-level may be impaired by evolutionary mechanisms. This thesis investigates evolutionary relationships of genus Berberis and their impacts on DNA barcoding. Phylogenetic relationships within genus Berberis in the Himalayas and the Hengduan Mountains are studied using whole plastid genomes and hundreds of nuclear loci. The phylogenies reveal pronounced biogeographic structures in the Sino-Himalayan region and suggest that the relatively recent orogeny of the Hengduan Mountains has a strong impact on in situ diversification of Berberis species. Low phylogenetic resolution at species-level may be explained by incomplete lineage sorting. The phylogenies suggest that evolutionary mechanisms hinder DNA barcoding to species-level and, therefore, a method is devised for identifying evolutionary lineages. A strategy for generating DNA barcodes based on diagnostic nucleotides using whole plastid genomes is presented. These barcodes are tested on commercial samples, and their utility for regulatory purposes outlined. Furthermore, species substitution and adulteration in global trade are evaluated with two different specimen identification methods. The first uses the phylogenetic placements of commercial samples of Berberis for specimen identification. The second approach applies DNA metabarcoding to commercial samples of Phyllanthus amarus. The results of these analyses show that congeneric species are in trade and further reveal a high congruence between species in global and local markets, emphasizing the dependency of global medicinal plant trade on local trade systems. Finally, sequencing data from genus Arabidopsis is analysed to identify the effect of assembling nuclear loci that belong to paralogous clusters on phylogenomic inference. Read mapping from cognate paralogues in Arabidopsis has little to no effect on outcomes from phylogenomic inference