Comprehensive analyses of molecular phylogeny and main alkaloids for Coptis (Ranunculaceae) species identification

• The interspecific relationships between molecular phylogeny and the main alkaloids in Coptis were analyzed.
• The gene constitution revealed the genetic characteristics of the genus Coptis species.
• The metabolic components of the genus Coptis are mainly affected by the environmental factors but not by the gene constitution.

The medicinal plants from the genus Coptis were widely applied in clinical treatment, but no stable and systemic methods have been established for species identification and quality evaluation. Although several analytical methods have been reported for the detection of alkaloids, so far no attempt has been made to analyze the interspecific relationships between molecular phylogeny and main alkaloids in Coptis. In this study, the phylogenetic relationships within the genus Coptis from China are resolved with high support. Coptis chinensis, Coptis deltoidea and Coptis omeiensis cluster together, and this clade (‘clade III’) is sister to Coptis teeta. Here, we provide evidences that the relationships inferred by chemical taxonomy are different to those of the present molecular phylogeny. Within clade III, C. deltoidea, C. omeiensis and C. chinensis are sister to C. teeta, while C. teeta shares more similar metabolic compounds with C. deltoidea, and C. omeiensis than with C. chinensis. Most likely, the metabolic components are mainly affected by environmental factors resulting in convergent evolution of alkaloid contents that do not reflect phylogenetic relationships.