Phylogenetic and mutation point analysis of DNA barcoding sequences in Solanum nigrum / 中草药

ABSTRACT

Objective: In this study, phylogenetic analysis was used to compare the ITSs and trnH-psbA sequences of 17 Solanum nigrum samples, providing the theoretic foundation to utilize their resources and evaluate their genuineness. Methods: PCR method was used to amplify the region of ITS and trnH-psbA, and the seqeucens of ITS1 + ITS2 and trnH-psbA were obtained after the amplified fragment sequences were blasted in NCBI database. The Neighbor joining (NJ) and maximum parsimony (MP) method were used to construct phylogenetic trees and Kimura two-parameter (K2-P) model was used to calculate the genetic distance of different samples. Clustal X and DNAman softwares were applied for multi-alignment of ITS1, ITS2, and trnH-psbA sequences from different samples. Results: The lengths of ITS1 and ITS2 sequences from 17 samples were 230 and 206 bp, respectively, and trnH-psbA sequences were 446 or 447 bp. ITS1, ITS2, and trnH-psbA had seven, two, and three mutation points, respectively. These 17 samples were clustered to three latitude-dependent groups based on both ITS1 + ITS2 and trnH-psbA sequences. Conclusion: Phylogenetic and mutation point analysis will provide the theoretic foundation to utilize the resources of Chinese S. nigrum, investigate their evolution, and evaluate their genuineness. The results of mutation point will also be used in the identification of related S. nigrum resources.