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Paphiopedilum venustum, an endangered wild resources, has high ornamental value and conservation biological value. Chloroplast genome (cpDNA), small with stable structure and high conserved in nature, has been widely used in plant phylogeny and species identification. Understanding the chloroplast genome structure of P. venustum is of great significance in revealing the phylogenetic relationship of Paphiopedilum. In this study, the whole chloroplast genome of P. venustum was sequenced by the Illumina sequencing technology, the chloroplast genome was annotated using GeSeq, BLAST and hmmer, the genome structure, gene number, repeats, codon usage bias, phylogenetic development were analyzed using the bioinformatics softwares such as MISA, codonW and Fasttree. The chloroplast genome of P. venustum had a conserved quadripartite structure, with a pair of inverted repeats (IRs) separated a large single copy (LSC) region and a small single copy (SSC) region from the small single-copy region (SSC), with a total length of 158 298 bp. The guanine and cytosine (GC) content of chloroplast protein coding genes was 35.4%, and 129 genes were annotated, including 79 protein coding genes, 38 tRNA genes, 8 rRNA genes, and 4 pseudogenes. 78 simple sequence repeat (SSR) loci were detected, most of which were mononucleotide repeats and dinucleotide repeats, accounting for 84.62% and 10.26% respectively. There were no pentanucleotide repeats, and most of the repeats were composed of A or T base. 32 high-frequency codons were identified, and 90.6% of them ended in A or U, preferred codons ending in A or U. The codon encoding leucine (Leu) had the highest frequency of use, while the codon encoding cysteine (Cys) had the lowest frequency of use. Phylogenetic tree was constructed by comparing the chloroplast genomes of 18 orchidaceae plants. It was found that the two species of Cypripedilum calceolus and C. tibeticum were separated from 16 species of Paphiopedilum and clustered into a single branch, and the genus of Paphiopedilum was divided into two groups, among which P. venustum and P. purpuratum were closely related. SSR and nucleotide polymorphisms can be used as molecular markers for germplasm identification and genetic diversity analysis of Paphiopedilum, which could provide a theoretical basis for germplasm identification and phylogeny of rare and endangered plant Paphiopedilum and its relatives, and lay a foundation for population restoration, biodiversity protection, innovative utilization and new variety breeding of Paphiopedilum.
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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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