Abstract
BackgroundAtractylodes 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.ResultsThe 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.ConclusionsOur 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.
Highlights
Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia
Six complete chloroplast genome sequences were deposited in GenBank with accession numbers MT834519 to MT834524
Six protein-coding genes, seven Transfer RNA (tRNA) genes and all four Ribosomal RNA (rRNA) genes are duplicated in the inverted repeat region (IR) regions
Summary
Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using highthroughput sequencing. Comparative chloroplast genome sequences provide an opportunity to discover the sequence variation and identify mutation hotspot regions, while detecting the gene loss and duplication events. Mutation hotspot regions and single sequence repeats (SSRs) obtained from the chloroplast genome sequences can be effective molecular markers for species identification and population genetics [12]. Traditional Chinese herbal medicines “Baizhu” and “Cangzhu” originate from Atractylodes [13]. It is the traditional medicine for treatment of gastroduodenal diseases. The genus Atractylodes was identified as early as 1838; the relationship between and within the genus has never ceased to be controversial
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