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Paris polyphylla var. alba is a medicinal plant commonly used in the southwest of China. This study characterized the complete chloroplast (cp) genome sequence of P. polyphylla var. alba to investigate its phylogenetic relationship in Melanthiaceae. The cp genome of P. polyphylla var. alba is 165,079 base pairs (bp) in length with 36.96% G + C content. The cp genome is divided into (a) large single copy (LSC) (84,393 bp), (b) small single copy (SSC) (16,066 bp), and (c) two inverted regions (32,310 bp). The cp genome contains 135 genes, including 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that P. polyphylla var. alba is closest to P. polyphylla var. emeiensis, and Paris had a close relationship with Trillium in Melanthiaceae. [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]