Chloroplast genomes of two Pueraria DC. species: Sequencing, comparative analysis and molecular marker development.

Puerariae lobatae radix (Ge-Gen in Chinese) and Puerariae thomsonii radix (Fen-Ge) are widely used as medicine and health products, particularly in Chinese medicine. Puerarin and daidzein are the primary bioactive compounds in Puerariae radix. These isoflavones have been used to treat cardiovascular and cerebrovascular diseases, hypertension, diabetes and osteoporosis. The content of puerarin in Ge-Gen is about six times higher than that in Fen-Ge, so its use has a higher pharmacological effect. It is therefore of great importance to effectively distinguish between these two species. However, because their basal plants, Pueraria lobata (Willd.) Ohwi and Pueraria thomsonii Benth., possess an extremely similar appearance, and detecting the level of chemical constituents is just a rough distinction, it is necessary to develop more efficient identification approaches. Here, the complete chloroplast (CP) genomes of P. lobata and P. thomsonii were deciphered, including sequencing, assembly, comparative analysis and molecular marker development. Results showed that they are 153,393 bp and 153,442 bp in length, respectively; both contain 124 annotated genes, including eight encoding ribosomal RNA (rRNA), 29 encoding transfer RNA (tRNA) and 87 encoding proteins. Phylogenetic analysis showed that they form a clade, indicating that they originate from the same ancestor. After obtaining ten intergenic/intronic regions with genetic distance greater than 0.5 cM, primers were designed to amplify regions of high variability in P. lobata and P. thomsonii. Finally, a 60 bp differential base fragment, located in the intron of rpl16, was developed as a molecular marker to efficiently distinguish between these two species.