The Chloroplast Genome Analysis Of Three Atractylodes Species,Iodes Cirrhosa And Leonurus Artemisia,and Software Development For Discovery Molecular Markers

As a plant organ for photosynthesis and energy transformation,chloroplasts play an important role in maintaining the survival and development of the Earth's living organisms.In recent years,with the rapid development of gene sequencing technology,more and more plant chloroplast genome information has been resolved.At present,the accurate identification and phylogenetic study of plants based on chloroplast genome has been favored by more researchers.It is considered as an effective method for the study of the plant identification and phylogenetic relationship.Given the importance of chloroplast genomes,the basic structure,genome composition and the structural variation of chloroplast genomes of five medicinal plants(Atractylodes lancea,Atractylodes chinensis,Atractylodes macrocephala,lodes cirrhosa and Leonurus japonicus)were analyzed based on the chloroplast genome information.The main results are as follows:1.In this study,the chloroplast genomes of three medicinal plants Atractylodes lancea,Atractylodes chinensis and Atractylodes macrocephala were obtained for the first time.The chloroplast genome maps were drawn and genome structures were analyzed.Molecular markers were developed to effectively distinguish three species and validated in 15 individuals of the genus Atractylodes.2.In this study,we constructed a molecular marker development method based on second-generation sequencing reads.This method is based on the following four principles:the larger inter nucleotide diversity among species,the smaller intra nucleotide diversity within the species,the larger difference between inter nucleotide diversity and intra nucleotide diversity and the shorter poly sequence length.In this study,we developed the molecular markers of Atractylodes based on this method and found the result are consistent with the manually developed Atractylodes molecular marker.The results show that the molecular marker development system based on second-generation sequencing reads constructed in this study has certain reliability.3.This study firstly determined the chloroplast genome of Iodes cirrhosa,and we analyzed the phylogenetic relationships based on the protein coding sequence,the complete nucleotide sequence and the ITS sequence,respectively.The phylogenetic trees provide that I.cirrhosa has more closer relationship with Eucommia ulmoides(Garryales)than the species from Aquifoliales,Sapindales and Celastrales.4.This study obtained the first complete chloroplast genome of Leonurus.The structure and gene composition of the chloroplast genome of Leonurus japonicus is highly conserved,and there is no deletion,contraction or expansion of IR region phenomenon such as Leguminosae and Campanulaceae.The phylogenetic position of Leonurus japonicus in Lamioideae subfamily was determined and the results showed that the genus of Leonurus is closely related to the geneus of Stachys in evolutionary relationship.