Molecular authentication of Paeonia species for paeonia radix production using plastid and nuclear DNA markers

Paeonia lactiflora is a perennial herbaceous plant popular in oriental medicine and as an ornamental plant. Two related species, P. veitchii and P. obovata, share several medicinal uses with P. lactiflora. To develop a molecular authentication system for these three Paeonia species, which are used to produce the Chinese herbal medicine Paeonia Radix, we generated super-barcode information. This included complete plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) from two accessions of P. lactiflora and one accession each of P. veitchii and P. obovata, using whole-genome sequencing data. The four plastomes range from 152,519 to 152,731 base pairs (bp) in length and have the same gene content and order. The 45S nrDNA transcriptional units range from 5879 to 6315 bp in length and show 33 SNPs among the three species. Phylogenetic analyses based on plastome and 45S nrDNA sequences clearly identified each species as a monophyletic group. Inter- and intraspecific polymorphisms were discovered among these three Paeonia species and Paeonia suffruticosa. Four molecular markers were developed to discriminate between P. lactiflora, P. veitchii, P. obovata, and P. suffruticosa, the main species used to produce Paeonia Radix in Korea and China. These markers successfully authenticated the species when applied to multiple herbal samples collected from various origins.