Yiheng Wang1, Sheng Wang1, Yanlei Liu2, Qingjun Yuan1, Jiahui Sun3, Lanping Guo4. 1. National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. 2. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. 3. National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. sunjh_2010@sina.com. 4. National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. glp01@126.com.
Abstract
BACKGROUND: Atractylodes DC is the basic original plant of the widely used herbal medicines "Baizhu" and "Cangzhu" and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. RESULTS: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. CONCLUSIONS: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.
BACKGROUND:Atractylodes DC is the basic original plant of the widely used herbal medicines "Baizhu" and "Cangzhu" and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. RESULTS: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. CONCLUSIONS: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.
Entities:
Keywords:
Chloroplast markers; Indel; Interspecific relationships; Simple sequence repeat; Traditional herbal medicine
Authors: Susann Wicke; Gerald M Schneeweiss; Claude W dePamphilis; Kai F Müller; Dietmar Quandt Journal: Plant Mol Biol Date: 2011-03-22 Impact factor: 4.076
Authors: Maoqin Xia; Minqi Cai; Hans Peter Comes; Li Zheng; Tetsuo Ohi-Toma; Joongku Lee; Zhechen Qi; Kamil Konowalik; Pan Li; Kenneth M Cameron; Chengxin Fu Journal: Ann Bot Date: 2022-07-19 Impact factor: 5.040