Study On The Complete Chloroplast Genome Of Magnolia Grandiflora Using The High-Throughput Sequencing Technology

The chloroplast (cp) is an important organelle found in plants wherephotosynthesis and energy transformation occurs. It is semiautonomousorganelle and is inherited in a maternal manner. Compared with the nucleargenome, the cp genome is smaller in size and more convenient to clone andgenetic manipulation. The cp has multiple copies in each cell, which canensure high expression of genes targeted to the cp. Targeted integration ortransgenes in the cp genome can avoid position effects and gene silencing.Matrilineal inheritance is allowing stable transgene expression without genecontamination. The chloroplast has a moderate rate of nucleotide evolution,but shows a big difference in the rate of divergence between coding andnon-coding regions. This makes the cp genome suitable for phylogeneticstudies at different taxonomic levels. The study on the cp genome helps us toadvance cp genetic engineering, molecular breeding, new molecular markersscreening and phylogenetic relationships constructing. Obtaining the cpcomplete genome is one premise of the cp genome research, which is based onthe extraction of adequate and pure cpDNA.In this paper, Magnolia grandiflora were took for example, and aprocess including cp genome’s extracting, sequencing, assembling, annotating,sequence analysing and phylogenetic tree constructing was established. Inthese research, through improved sucrose-gradient centrifugation, a high quality cpDNA was obtained. Besides, two ways used in our laboratory forassembling and annotating with or without a referenced sequence rspectivelywere summarized. The discussion about contraction and expansion of the IRregions provided information to demonstrate the IR boundary variations of cpgenome structures. SSR analysis can lay a foundation for cp molecularmarkers. Phyletic evolution is a significant application in cp genome, andsuitable for studying the cp genome with lower taxonomic level. Comparativestudy in chloroplast genomes plays an important role in the speciesidentification based on the cp genome data.M. grandiflora is an important medicinal plant, so it was chose for theobject of this study. And its cp genome was sequenced with a454sequencingplatform and its genome structure was compared with other related species.The results showed that the gene category, number and GC content of M.grandiflora were similar to those of other species genomes in the same family.In addition, it was indicated that the cp genome size and the position of the IRborder were closely related to the length of ycf1gene. Phylogenetic analysesbased on the shared genes using MP tree and ML tree provided strongevidence for the phylogenetic position of M. graniflora. In a word, this studyprovides valuable information for good varieties’ breeding, cp geneticengineering, good molecular markers developing and phylogenetic analysing.