Complete chloroplast genome sequencing and phylogeny of wild Atractylodes lancea from Yuexi, Anhui province.
10.19540/j.cnki.cjcmm.20221014.102
- Author:
Jian-Peng HU
1
;
Lu JIANG
1
;
Rui XU
1
;
Jun-Xian WU
1
;
Feng-Ya GUAN
1
;
Jin-Chen YAO
1
;
Jun-Ling LIU
2
;
Ya-Zhong ZHANG
2
;
Liang-Ping ZHA
1
Author Information
1. School of Pharmacy, Anhui University of Chinese Medicine Hefei 230012, China.
2. Anhui Institute for Food and Drug Control Hefei 230051, China.
- Publication Type:Journal Article
- Keywords:
Atractylodes lancea;
SSR;
chloroplast genome;
codon bias;
phylogenetic analysis
- MeSH:
Phylogeny;
Atractylodes/genetics*;
Genome, Chloroplast;
Whole Genome Sequencing;
Microsatellite Repeats;
Lamiales
- From:
China Journal of Chinese Materia Medica
2023;48(1):52-59
- CountryChina
- Language:Chinese
-
Abstract:
This study investigated the choroplast genome sequence of wild Atractylodes lancea from Yuexi in Anhui province by high-throughput sequencing, followed by characterization of the genome structure, which laid a foundation for the species identification, analysis of genetic diversity, and resource conservation of A. lancea. To be specific, the total genomic DNA was extracted from the leaves of A. lancea with the improved CTAB method. The chloroplast genome of A. lancea was sequenced by the high-throughput sequencing technology, followed by assembling by metaSPAdes and annotation by CPGAVAS2. Bioiformatics methods were employed for the analysis of simple sequence repeats(SSRs), inverted repeat(IR) border, codon bias, and phylogeny. The results showed that the whole chloroplast genome of A. lancea was 153 178 bp, with an 84 226 bp large single copy(LSC) and a 18 658 bp small single copy(SSC) separated by a pair of IRs(25 147 bp). The genome had the GC content of 37.7% and 124 genes: 87 protein-coding genes, 8 rRNA genes, and 29 tRNA genes. It had 26 287 codons and encoded 20 amino acids. Phylogenetic analysis showed that Atractylodes species clustered into one clade and that A. lancea had close genetic relationship with A. koreana. This study established a method for sequencing the chloroplast genome of A. lancea and enriched the genetic resources of Compositae. The findings are expected to lay a foundation for species identification, analysis of genetic diversity, and resource conservation of A. lancea.
