Phylogenetic analysis of chloroplast genome of Tussilago farfara L.
10.16438/j.0513-4870.2023-0437
- VernacularTitle:款冬叶绿体基因组序列特征及其系统发育分析
- Author:
Yi-yao JING
1
;
Ben-xiang HU
1
,
2
,
3
;
Xiao-ying CHEN
1
;
Hai-yue JI
1
,
2
,
3
;
Yao LUO
1
;
Jia-zhou SHI
1
;
Bang-qing WANG
4
;
Gang ZHANG
1
;
Jing GAO
1
;
Bing-yue YANG
1
;
Liang PENG
1
Author Information
1. Key Laboratory for Research of Qin medicine of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi Qinling Application Development and Engineerig Center of Chinese Herbal Medicine, College of Pharmacy, Shaanxi University of Chinese Medicine, Xi′an 712046, China
2. Shaanxi Institute of International Trade &
3. Commerce, Xi′an 712046, China
4. Hanzhong Science and Technology Coordination Center, Hanzhong 723000, China
- Publication Type:Research Article
- Keywords:
italic>Tussilago farfara L.;
Compositae;
chloroplast genome;
sequence analysis;
phylogeny
- From:
Acta Pharmaceutica Sinica
2023;58(11):3439-3448
- CountryChina
- Language:Chinese
-
Abstract:
italic>Tussilago farfara L. is a perennial herb of Tussilago genus in the Compositae family. Its dried buds and leaves have good biological activities and have a long history of medicinal use in China and Europe. In this paper, we investigated the whole chloroplast genome characteristics, sequence duplication, structural variation and phylogeny of the Tussilago farfara L. After sequencing the Tussilago farfara L. chloroplast genome using Illumination technology, the complete Tussilago farfara L. chloroplast genome was further obtained by assembly and annotation, followed by a series of inverted repeat-large single copy/small single copy region contraction and expansion analysis, genome sequence variation, etc. The sequences of 13 homologous plants downloaded from NCBI were used to construct a neighbor-joining phylogenetic tree. The results showed that the total GC content of the chloroplast genome was 37.4% and the length was 150 300 bp; 125 genes were annotated, including 82 protein-coding genes, 35 tRNAs and 8 rRNAs; 148 (simple sequence repeats, SSR) loci were detected, and the relative synonymous codon usage showed that 31 codons out of 64 codons had a usage of >1. In the phylogenetic analysis, the chloroplast genomes of the seven species of Asteraceae, including the Yulin Tussilago farfara L., were highly conserved, and the sequence variation of the (large single-copy, LSC) and (small single-copy, SSC) regions was higher than that of the (inverted repeat, IR) region. This is in general agreement with the reported phylogeny of Yulin Tussilago farfara L. In this study, we obtained a high quality chloroplast genome and analyzed its genome characteristics, codon preference, SSR characteristics, SC/IR boundary, sequence variation and phylogeny, which can provide a basis for species identification, genetic diversity analysis and resource development of this medicinal plant.
