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Paris polyphylla var. alba, a medicinal plant of Melanthiaceae, is classed as the national second-grade protected species of China. With the increasing demand for raw materials of Rhizoma paridis, the wild resources of P. polyphylla var. alba have been seriously damaged. In order to protect the genetic resources and clarify the systematic positon of this species, Illumina Hiseq X Ten platform was used to sequence the chloroplast (cp) genome. The structural characteristics of the complete cp genome sequence and phylogenetic relationship of P. polyphylla var. alba in Paris were analyzed. The results showed that the cp genome was 163 944 bp in length with a typical quadripartite structure with a large single-copy (LSC) region of 84 179 bp, a small single-copy (SSC) region of 12 967 bp, and a pair of 33 399 bp inverted repeats (IRs). The genome contained 134 genes, including 88 protein-coding genes (PCGs), 38 tRNA genes and 8 rRNA genes. A total of 645 long repeats and 97 simple sequence repeats (SSRs) loci were detected in the complete cp genome, in which forward and palindromic repeats were the mainly long repeat types, and most of SSRs had A/T base preference. Phylogenetic analysis based on the complete cp genomes showed that Paris formed a monophyletic group, and could be further divided into five major clades corresponding to five sections, respectively. The varieties of P. polyphylla are located in Sect. Euthyra, but are not clustered a monophyletic group, and P. polyphylla var. alba is closely related to P. mairei. This study would provide a scientific basis for studying the phylogeny, species identification and resource conservation of Paris.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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