ABSTRACT
This study is to identify Chinese medicinal materials Rhizoma et Radix Heraclei, Angelicae Sinensis, Radix Angelicae Pubescentis and Rhizoma et Radix Notopterygii based on ITS2 and its secondary structure. Total 26 ITS sequences of 7 species were downloaded from GenBank, the ITS2 sequences were annotated by HMMer method. The NJ phylogenetic tree was built by MEGA software, the intraspecific and interspecific K2P genetic distance were analyzed by MEGA as well. The ITS2 secondary structures of all taxa were predicted by ITS2 database. Sequence matrix of primary structure and secondary structure was aligned by 4Sale software. And the profile neighbor joining (PNJ) phylogenetic tree was constructed via the the ProfDistS software based on the distance method. The results show that, the average interspecific genetic distance was far greater than the average intraspecific genetic distance, an obvious barcoding gap was noted among all taxa; NJ tree showed that all species were clustered into seperate branches; each species had different secondary structures; the PNJ tree showed higher resolution than NJ tree. Therefore, ITS2 is suggested to be used as a barcode for distinguishing the original plants of Rhizoma et Radix Heraclei, Radix Angelicae Sinensis, Radix Angelicae Pubescentis and Rhizoma et Radix Notopterygii in this study, this provides some scientific basis for classification and accurate identification of these Chinese medicinal materials.