| Compositae is a family which has various kinds of medicinal species. Dendranthema morifolium and Dendranthema indlcum which are the main traditional Chinese medicines in Dendranthema of Compos itae, have experienced all kinds of variation for a long time because of the influences from natural hybrid, artificial selection and environmental conditions, etc. It is difficult to reveal their essence in biology by using traditional identification methods in medicinal herbs. It's necessary to explore a more effective way to identify such kind of closely related plants and different populations from one specie.DNA barcoding is a technology of rapid and accurate species identification and recognition using a relatively general, with sufficient variation, easy expansion and relatively short DNA sequence. On early research of DNA barcoding in Compos itae species, ITS2sequence has the optimal comprehensive evaluation index in the popular candidate sequences. So we have used ITS2sequence to identify closely related species in Compositae, and judge the identification efficiency among closely related species and intraspecific samples. Through extracting the total DNA from63 samples in Compositae, including11species in Dendranthema and1sample in Matricaria, ITS2sequences was amplified and sequenced. After jointing the fragments as a whole sequence, we have got ITS2sequences of the63samples. The results of data analysis show that ITS2sequence of the Dendranthema plants variants less, and which can correctly identify genus reached96.8%, can correctly identify species reached87.3%, while the efficiency of distinguishing the difference among interspecific and intraspecific samples is only12.7%.Chloroplast has independently genomic DNA, and which is inherited as maternal genetic primari ly. Its structure and function are highly conservative. The length of chloroplast genome is more than100kb, and most of DNA barcodes in plants come from chloroplast genome. As its better resolution and generality than traditional DNA barcoding, it may become a potential super barcode in species identification, and has comprehensive application prospects in screening better plant DNA barcodes, phylogenetic analysis, and chloroplast engineering. And it shall play an enormous role on the study of authentic medicinal materials.We put an emphasis on the chloroplast genome of medicinal plants, Dendranthema morifolium, Dendranthema indicum var. aroma ticum and3populations of Dendranthema indicum from Jiangsu, Henan and Zhejiang, which all come from Dendranthema in Compositae. After extracting chloroplast genome DNA of the5samples and purifying them, the author has got5complete chloroplast genome sequences by high-throughput pyrosequencing to sequence and jointing the contigs. After having annotated them successfully, we have obtained their gene maps of chloroplast genome. Preliminary comparative analysis on genome structure, gene type of these5samples of chloroplast have been accomplished, which have laid sol id foundat ion for the later work of better DNA barcodes screening in traditional Chinese medicines and the study on authentic medicinal materials. In addition, we have selected10chloroplast genome sequences, including the5Dendranthema samples,4Compositae species released on NCBI, and Magnolia liliflora chloroplast genome we previously have gained as outgroup. Carrying on phylogenetic analysis on the53protein-coding genes of the10samples, we have respectively constructed maximum parsimony (MP) tree and maximum likelihood (ML) tree. The results show that the chloroplast genome sequences can successfully identify different species in the Compositae plants, Dendranthema morifolium and Dendranthema indicum can be distinguished effectively, and three different populations of Dendranthema indicum cluster into one branch. The above all prove that chloroplast genome have enormous potential to became a super barcoding in species identification.
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