Comparative analysis of three complete chloroplast genomes of Inula genus with phylogenetic analysis of 49 plants from Carduoideae
10.16438/j.0513-4870.2019-0774
- VernacularTitle:旋覆花、湖北旋覆花和线叶旋覆花的叶绿体基因组比较分析和系统发育研究
- Author:
Xi WU
1
;
Mei JIANG
1
;
Hai-mei CHEN
1
;
Li-qiang WANG
1
;
Lin-fang HUANG
1
;
Chang LIU
1
Author Information
1. Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
- Publication Type:Research Article
- Keywords:
italic>Inula japonica;
italic>Inula hupehensi;
italic>Inula linaariifolia;
chloroplast genome;
repeat sequence;
phylogenetic evolution
- From:
Acta Pharmaceutica Sinica
2020;55(5):1042-1049
- CountryChina
- Language:Chinese
-
Abstract:
italic>Inula japonica, Inula hupehensis and Inula linaariifolia are all medicinal plants of Inula L. in the Compositae family, and Inula hupehensis is endemic to China. In order to compare their genomic sequence differences and provide scientific basis for their germplasm conservation and development, we obtained and analyzed the complete chloroplast genomes of these three species. Total DNAs were extracted from fresh leaves and subjected to next-generation DNA sequencing. NOVOPlasty was used to assemble the chloroplast genomes from the sequence reads. CPGAVAS2 was used to annotate the genes and repeats in each genome. Lastly, phylogenomics analysis was conducted using RAxML. The results showed that the total length of the chloroplast genome of Inula japonica, Inula hupehensis and Inula linaariifolia is 150 754, 150 909, and 150 812 bp respectively, each consisting of a large single copy region, a small single copy region and a pair of inverted repeat regions. In addition, the G/C content of all three chloroplast genomes was approximately 37.7% and each encoded 111 unique genes, including 79 protein-coding, 28 tRNA and 4 rRNA genes. Meanwhile, 32, 33, 34 simple repeat sequences, 18, 22, 18 tandem repeat sequences and 33, 37, 38 scattered repeat sequences were identified in three species. Phylogenomic analysis showed that all three species of Inula L. and Pluchea indica were clustered together, with the relationship between Inuleae and Senecioneae closer, suggesting that Inuleae may have originated from the Senecioneae, not the Cardueae. The data in this study not only enriches the chloroplast genome database of Inula L., but also lays the foundation for the future studies of species identification, phylogenetic relationships, evolution history and genetic diversity of Inula species.
