Abstract
BackgroundStauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily.ResultsA series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages.ConclusionsThis study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
Highlights
Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China
A total of 44,897,908 paired-end reads were retrieved with a sequence length of 150 bp, while a total of 41,809,601 of high-quality reads were used for mapping
The Stauntonia chinensis chloroplast genes encoded a variety of proteins, which were mostly involved in photosynthesis and other metabolic processes, including large rubisco subunit, thylakoid proteins and subunits of cytochrome b/f complex (Table 2)
Summary
Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. Belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. The complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. The molecular techniques are required to analyze the genetic diversity and phylogenetic relationship of these plants. Chloroplasts contain their own genome, composing of approximately 130 genes, which has a typical quadripartite structure consisting of one large single copy region (LSC), one small single copy region (SSC) and a pair of inverted repeats (IRs) in most plants [4,5,6]. The complete chloroplast genome has been considered to be informative for phylogenetic reconstruction and testing lineagespecific adaptive evolution of plants
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