Characterization and phylogenetic analysis of the complete chloroplast genome of Salvia apiana Jepson
10.16438/j.0513-4870.2023-1056
- VernacularTitle:白鼠尾草叶绿体基因组序列特征与系统进化分析
- Author:
Zhen-xi FANG
1
;
Qian JI
1
;
Jia-dong HU
2
;
Wan-sheng CHEN
2
;
Qing LI
2
Author Information
1. Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
2. Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
- Publication Type:Research Article
- Keywords:
italic>Salvia apiana Jepson;
chloroplast genome;
sequence characterization;
codon preference;
phylogenetic analysis
- From:
Acta Pharmaceutica Sinica
2024;59(5):1484-1493
- CountryChina
- Language:Chinese
-
Abstract:
italic>Salvia apiana Jepson, commonly known as white sage, is a perennial sub-shrub of the Salvia genus in the Lamiaceae family with a long medicinal history. In this study, the complete chloroplast genome of S. apiana was sequenced using PacBio HiFi third-generation sequencing technology. The physical map of the genome was constructed, and the sequence structure features, codon preference, and repetitive sequences were analyzed. Furthermore, a comparative analysis of the chloroplast genome and phylogenetic evolution with closely related species within the same genus was conducted. The chloroplast genome of S. apiana was found to have a length of 151 701 bp (GenBank accession number: OR389048), with a typical quadripartite structure and a GC content of 38.06%. A total of 132 genes were annotated, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among them, 17 genes contained introns, and 18 genes were present in duplicate copies. Codon preference analysis revealed a preference for codons ending with A or U. Analysis of repetitive structures in the S. apiana chloroplast genome identified 170 simple sequence repeat (SSR) sites and 65 scattered repeat sequences, with the majority of SSR sites composed of A and T. Phylogenetic analysis of the complete chloroplast genomes of 21 species within the same genus showed that S. apiana is most closely related to Salvia hispanica Ettling. ex Willk. & Lange, Salvia leucantha Cav., and Salvia tiliifolia Vahl. Comparative analysis of the chloroplast genomes revealed slight contraction and expansion of the inverted repeat (IR) boundaries in S. apiana, as well as multiple highly variable regions in the chloroplast genome sequence. This study establishes a method for de novo assembling the chloroplast genome of S. apiana using third-generation sequencing data and provides a comprehensive analysis of its chloroplast genome, which can serve as a theoretical basis for studies on chloroplast genetic engineering, genetic diversity analysis, molecular breeding, and species identification.
