Comparative and Phylogenetic Analysis of Chloroplast Genomes of Two Medicinal Species of Spatholobus

Abstract Background The vine stem of Spatholobus suberectus Dunn (S. suberectus), called “JiXueTeng”, has been used as a significant medicine for thousands of years in China. However, reliable field identification of this medicinal plant remains problematic, inaccurate identification may cause serious adverse effects in the functions of the drug and may affect the clinical medication reviews. Objective To ensure use of the exact medicine and implement protective legislation, it is imperative to obtain the chloroplast (cp) genome of S. suberectus, which can be used as a valuable resource for species identification and phylogenetic analysis. Methods In this study, the complete cp genomes of S. suberectus (152 173 bp (base pair)) and S. pulcher (151 099 bp) were assembled for the first time by using next-generation sequencing (NGS) technology to gain abundant information on the genus of Spatholobus. And some bioinformatics softwares were used for data filtering, assembling and analyzing. Results We found the G and C contents of S. suberectus and S. pulcher were close, 35.19% and 35.37%, respectively. The noncoding regions were more divergent than coding ones. Moreover, we revealed eight divergence hotspots (trnH, trnK-rbcL, trnL-rbcT, psbD-trnT, trnC-rpoB, atpI-atpH, ycf4, and trnL-rpl32) which might be used as candidate molecular markers for Spatholobus identification. The analysis of the phylogenetic relationship indicated that two Spatholobus species were clustered together and two Spatholobus species was sister to the Cajanus. Conclusion The findings of this study were conducive to species identification and phylogenetic research of Spatholobus and provided valuable resources for finding the substitution of S. suberectus. Highlights We assembled the complete cp genomes of S. suberectus and S. pulcher for the first by using next-generation sequencing.