Chloroplast Genome Of Rehmannia(Orobanchaceae)

Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China.Its phylogenetic position and infrageneric relationships maintain uncertain due to the potential hybridization and polyploidization.The phylogenetic position and interspecific relationship of Rehmannia were not well solved based on chloroplast genes or nuclear DNA fragments.The data of chloroplast genome is an important source for exploring the evolution and phylogenetic relationship of unresolved taxa.In this study,high-throughput sequencing technologies were used to obtain the chloroplast genome sequences of six Rehmannia species and to carry out the comparative genomics analysis.The phylogeny of Orobanchaceae was reconstructed based on the 23 chloroplast genome sequences published.The main contents and the results of this research are as follows:Bioinformatics analysis indicated that the cp genomes of six Rehmannia species exhibited typical quadripartite and circular structures with good synteny of gene order.The complete genomes ranged from153,622 bp to 154,055bp in length,the LSC,SSC and IR ranged from 84,605-84,966bp,17,579-17,680bp,25666-25735bp in length respectively.Each of the genome including 133 genes encoding 88 proteins,37 tRNAs,and 8 rRNAs,18 of these genes were duplicated in IR.The base composition has high similarity in six cp genome sequences,amino acids and codon usage are also coincident,both prefer to use A,T bases.Cp genome size variation of Rehmannia was mainly ascribed to the expansion and contraction of the border regions between the inverted repeat(IR)region and the single-copy(SC)regions.By comparing the IR/SC border Rehmannia chloroplast genome found that LSC/IR is more different than SSC/IR.The mVISTA analyses with mutation rate statistics including the coding regions and non-coding regions show that the sequence of Rehmannia chloroplast genomes are at low extent of genetic differentiation,inversion repeat region are more conservative than single copy region,coding regions are more conservative than non-coding regions.Despite of the conserved structure in Rehmannia cp genomes,sequence variations provide useful phylogenetic information.A mutation hot spots region was detected,and eight coding regions and nine non-coding regions were selected to be candidate for DNA barcoding.The chloroplast genome of Rehmannia contains 411 repeat sequences,the types and distribution in interspecific highly similar,while the SSR of single-base type is the majority,mainly for A or T.Among the substitution events of the CDS region,all of the pairwise sequence comparisons showed that the number of synonymy substitution and synonymous substitution exist heterogeneity between the genes and species.Rehmannia solanifolia and Rehmannia henryi,Rehmannia elata and Rehmannia chingii,which possess the coincident substitution patterns respectively,while Rehmannia glutinosa and Rehmannia piasezkii possess the different substitution pattern seperately.Three genes(rpoA,rpoC2,accD)were under positive selection pressure.Phylogenetic trees of 23 Lamiales species reconstructed based on the four dataset(complete sequence,protein-coding sequences,large single-copy region,small single-copy region)of complete cp genomes suggested that Rehmannia was a monophyletic group with high bootstrap value.The phylogenetic trees based on complete sequence and protein-coding sequences demonstrated that Rehmannia was sister to the clade of Lindenbergia and the parasitic taxa of remaining in Orobanchaceae,which consistent with APG IV classification results.The interspecific relationships within Rehmannia were completely different with the previous studies:R.solanifolia and R.henryi were grouped into one branch sister to the remain species.R.glutinosa and R piasezkii were successive sisters to R.elata-R.chingii clade.