Comparative Transcriptome Analysis On Five Species Of Rehmannia

Rehmannia contains five herbaceous species,two tetraploid species(Rehmannia solanifolia and Rehmannia glutinosa)and three diploid species(Rehmannia chingii,Rehmannia henryi,and Rehmannia piasezkii).All are endemic to China except Rehmannia glutinosa extending its range to North Korea and Japan.Although there have been a large number of studies based on morphological,biochemical and molecular methods to determine the relationships among species of Rehmannia,the interspecific relationship of the genus is still need to be clarified due to limited data.In this study,RNAseq technology was used to analyze the transcriptome of roots,flowers and leaves from five species.The clean reads from root,flower and leaf were assembled into unigenes and remove redundant sequences.The total of 88,719 unigene sequences were obtained from Rehmannia chingii with the average length of 687 nt,N50 length of 1230 nt;the total 82,843 unigene sequences were obtained from R.henryi with the averge length of 698 nt,N50 length of 1246 nt;the total unigene sequences 72,494 points were obtained from R.solanifolia with the averge length of 718 nt,N50 length of 1373 nt;the total unigene sequences 85,860 sequence were obtained from R.glutinosa with the averge length of 690 nt,N50 length of 1213 nt;the total unigene sequences 92,205 points were obtained from R.piasezkii with the averge length of 677 nt,N50 length of 1202 nt;All redundant unigenes of five species of Rehmannia were reassembled and used for comparative transcription analysis between Rehmannia with other plants.The assembled unigenes were compared with Nr,GO,KEGG,COG databases to obtain complete gene function annotation,to acquire pharmaceutical metabolic pathway of Rehmannia,to analyze the phylogenetic relationships and to identify the key metabolic targets associated with important pharmaceutical traits of Rehmannia.Orthologous genes were selected and used to construct phylogenetic tree among the five species of Rehmannia.Rehmannia piasezkii was the basal taxon in the genus,while diploid Rehmannia chingii and Rehmannia henryi,tetraploid Rehmannia solanifolia and Rehmannia glutinosa formed a sister group,respectively.Proteins with important functions are usually more conservative,which tend to undertake selected in the evolutionary history.Ka/Ks value is widely used as indicator of whether the protein coding genes are subjected to natural selection pressure.In diploid species of Rehmannia,the orthologous genes undertaking purified selection have similar number to those with positive selection.In two tetraploid species,Rehmannia glutinosa and the Rehmannia solanifolia have more orthologous genes experienced purified selection,supporting their close phylogenetic relationships.After analysis of the pathway of the orthologous genes in Rehmannia,we found that mannosyltransferase gene was up-regulated in teraploid species,and down-regulated in the diploid species,indicating that the metabolic intensity of mannose has increased after genome duplication with the change of root traits.