Chloroplast Genome Structure of Stemona tuberosa and Phylogenetic Analysis Based on PacBio Sequencing
10.13422/j.cnki.syfjx.20230616
- VernacularTitle:基于PacBio测序的对叶百部叶绿体基因组结构及系统发育分析
- Author:
Yan LIAN
1
;
Feng HUANG
1
;
Wentao ZHU
2
;
Xiaofen LIU
1
;
Hao WU
1
;
Guihua JIANG
1
;
Xianmei YIN
1
Author Information
1. Key Laboratory of Standardization of Chinese Medicine， State Key Laboratory of Southwestern Chinese Medicine Resources， School of Pharmacy， Chengdu University of Traditional Chinese Medicine， Chengdu 611137， China
2. Sichuan Academy of Chinese Medicine Sciences， Chengdu 610041， China
- Publication Type:Journal Article
- Keywords:
Stemona tuberosa;
chloroplast genome;
PacBio sequencing;
phylogeny
- From:
Chinese Journal of Experimental Traditional Medical Formulae
2023;29(14):123-132
- CountryChina
- Language:Chinese
-
Abstract:
ObjectiveTo obtain high-quality chloroplast genome information on Stemona tuberosa and clarify its structure， sequence features， and phylogenetic status. MethodThe Illumina NovaSeq 6000 and PacBio RS Ⅱ platforms were used for library construction and sequencing of S. tuberosa， respectively. The data from both sequencing platforms were combined and subjected to bioinformatics analysis for genome assembly and base correction， resulting in a high-quality chloroplast genome. Subsequently， sequence features， repetitive sequences， gene diversity， and phylogeny were analyzed. ResultThe chloroplast genome size of S. tuberosa was determined to be 154 379 bp. The structure of the chloroplast genome followed the typical quadripartite circular form， consisting of a pair of inverted repeat regions （IRs） with a length of 27 074 bp， a small single-copy region （SSC） of 17 924 bp， and a large single-copy region （LSC） of 82 307 bp. The average GC content was 37.86%. A total of 121 genes were annotated， including 30 tRNA genes， four rRNA genes， and 87 protein-coding genes. Among them， six tRNA genes and 12 protein-coding genes contained introns. In the chloroplast genome of S. tuberosa， 49 long repetitive sequences and 59 single-nucleotide simple sequence repeats （SSRs） were identified. Comparative analysis of chloroplast genomes among four Stemona species revealed high diversity in the ycf1 and ndhF genes. The phylogenetic tree constructed based on the chloroplast genome showed consistent classification with the current taxonomic status of S. tuberosa. ConclusionThe high-quality chloroplast genome of S. tuberosa was successfully assembled， providing valuable information on the structure and sequence features of chloroplast genomes in four Stemona species， including S. tuberosa. These findings lay a foundation for the identification， evolution， and phylogenetic studies of medicinal plants in the genus Stemona.
