Characterization and Phylogenetic Analysis of the First Complete Chloroplast Genome of Shizhenia pinguicula (Orchidaceae: Orchideae)

作者：Yuan Chen, Yanlin Zhao, Quan Yan, Wei Wu, Qingqing Lin, Guoqiang Chen, Yanfang Zheng, Mingqing Huang, Shiming Fan, Yanxiang Lin · 发表于：Genes · 年份：2024 · DOI：10.3390/genes15111488 · 被引用次数：6 · 研究领域：Plant and animal studies、Biological and pharmacological studies of plants、Genomics and Phylogenetic Studies

Background: Genomic analysis is crucial for better understanding the evolutionary history of species and for their conservation. Shizhenia pinguicula is a rare medicinal plant endemic to China. However, the complete chloroplast genome of this species has not been reported to date. Insufficient genomic research on S. pinguicula has hindered effective conservation efforts for this valuable plant. Methods: In this study, we sequenced and assembled the first complete chloroplast genome of S. pinguicula using Illumina sequencing technology. We conducted a comparative analysis of its chloroplast genome with related species and reconstructed phylogenetic relationships. Results: The chloroplast genome of S. pinguicula exhibited a typical quadripartite structure with a length of 158,658 bp. A total of 123 genes, 118 simple sequence repeats, and 51 dispersed repetitive sequences were identified. The inverted repeat boundaries were significantly expanded, along with the pseudogenization and loss of multiple NDH genes. Codon usage bias is primarily influenced by natural selection and other factors, with the ycf3 gene under positive selection. Additionally, 10 hypervariable regions were detected for species identification and evolutionary studies. Phylogenetic analysis indicated that Ponerorchis gracilis and Hemipilia yajiangensis form a clade, with S. pinguicula as their sister species, located at the basal position of the Ponerorchis-Hemipilia alliance. Conclusions: The chloroplast geno...