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Multi-component determination and bioassays used for the quality control of traditional Chinese medicine (TCM) may have certain shortcomings. The effect-constituent index (ECI) is a quality evaluation index weighted by chemical composition analysis and effect detection. This index can be established by the dose-effect relationship of the active ingredients in TCM. In this study, Paris polyphylla var. yunnanensis (PY) was selected as the representative drug. Chemical evaluation and bioactivity evaluation were combined to establish the ECI, to compensate for the deficiency of a single evaluation method to some extent, and can be related to the efficacy of PY, in order to improve its quality standard. The ECI not only reflects the contribution of component content to the quality of PY, but also relates to clinical efficacy and reflects the influence of different components on the biological activity. Moreover, this study provided a reference method for the quality control of other TCMs. [Display omitted] • The effect-constituent index was applied to Paris polyphylla var. yunnanensis. • The results of chemical analysis and biological evaluation were combined. • Reflect contribution of component content and impact of components on bioactivity. • Provide a reference method for the quality control of other TCMs. [ABSTRACT FROM AUTHOR]

• Chloroplast genome sequences of five endangered Paris species were de novo assembled. • Subgenera Paris sensu strict is sister to the Daiswa and Trillium. • Phylogeny of genus Paris was inferred using protein-coding genes sequences. • Divergence times of Paris were inferred based on molecular evolution. Paris L. genus has been a precious traditional herb for more than 2000 years in China. However, due to overexploitation and habitat destruction, Paris is threatened by extinction. Similar morphological features cause the classification of Paris species in dispute. The chloroplast (cp) genome approach has been used to investigate the evolution of Paris. However, some studies confirm that the cp genome may result in misleading relationships because of the length variation, gaps/indels deletion, and incorrect models of sequence evolution in concatenated datasets. Therefore, there is a high demand for a reconstructed phylogenetic relationship and developed genetic markers to conserve these species. Recent studies have demonstrated that the protein-coding genes could provide a better phylogenetic relationship in the phylogenetic investigation. In this study, the complete cp genomes of five species were characterized, and the length of five cp genomes ranges from 162,927 bp to 165,267 bp, covering 89 protein-coding genes, 38 tRNA, and eight rRNA. The analysis of the repeat sequences, codon usage, RNA-editing sites, and comparison of cp genomes shared a high degree of conservation. Based on the protein-coding genes, the phylogenetic tree confirmed Paris 's position in the order Melanthiaceae, providing maximum support for a sister relationship of the subgenera Paris sensu strict (Paris s.s.) with the Daiswa and Trillium. In addition, the molecular clock showed that subgenus Paris was inferred to have occurred at about 52.81 Mya, whereas subgenus Daiswa has originated at 24.56 Mya, which was consistent with the phylogenetic investigation. This study provided a valuable insight into the evolutionary dynamics of cp genome structure in the family Melanthiaceae, and it also contributes to the bioprospecting and conservation of Paris species. [ABSTRACT FROM AUTHOR]