Analysis on structure and phylogeny of complete chloroplast genomes in Psammosilene tunicoides
10.7501/j.issn.0253-2670.2019.22.022
- Author:
Ya-Fang GAO
1
Author Information
1. Faculty of Traditional Chinese Pharmacy, Yunnan University of Traditional Chinese Medicine
- Publication Type:Journal Article
- Keywords:
Caryophyllaceae;
Complete chloroplast genome;
Dianthus longicalyx;
Phylogeny;
Psammosilene tunicoides W. C. Wu et C. Y. Wu
- From:
Chinese Traditional and Herbal Drugs
2019;50(22):5532-5536
- CountryChina
- Language:Chinese
-
Abstract:
Objective: To obtain the structural characteristics of chloroplast genome in Psammosilene tunicoides and analyze its phylogenetic position within the family of Caryophyllaceae. Methods: High-through-put sequencing technology and bioinformatic analysis softwares were used to analyze the structures of complete chloroplast genome of P. tunicoides. RAxML 8.2.11 software was utilized to reconstruct the Caryophyllaceae phylogentic tree with Amaranthus hypochondriacus as outgroup. Results: The complete chloroplast genome was 153 977 base pairs (bp) in size, including two inverted repeat (IR, 26 033 bp) regions separated by one large singe copy region (LSC, 84 385 bp) and one small singe copy region (SSC, 17 526 bp). The genome encoded 125 genes, of which 109 were unique, including 75 protein-coding genes (PCGs), 30 tRNA genes and 4 rRNA genes. The overall GC content of P. tunicoides was 36.5%, while those of IR regions (42.4%) were higher than LSC (34.2%) and SSC (30.1%) regions. The phylogenetic tree showed that P. tunicoides and Dianthus longicalyx were sister groups with 100% bootstrap value. All nodes of the phylogenetic tree of Caryophyllaceae were of high supports, and the ML tree had good resolution to reflect the phylogeny relationship among the Caryophyllaceae. Conclusion: The complete chloroplast genome of P. tunicoides and the phylogenetic relationship within Caryophyllaceae were analyzed in this study. The results will provide effective molecular information for further studies on evaluation of germplasm and molecular phylogeny of Caryophyllaceae.
