李属植物梅(Prunus mume Sieb. et Zucc)，杏（Prunus armeniaca.Lindl），李（Prunus salicina Lindl）是我国重要的果树。不仅可以鲜食，还能够加工果酒和蜜饯等，具有重要的经济和研究价值。而叶绿体基因组有体积小，细胞质遗传，核苷酸替换率低，单倍体性质和高度保守的基因组结构等特点，是研究植物育种，系统发育及地理驯化理想基因组。本研究通过比较采用叶绿体试剂盒，高盐-低pH配合Percoll密度梯度以及改良高盐-低pH三种方法分离叶绿体的效果，荧光显微镜检测叶绿体完整性，琼脂糖凝胶电泳与核酸检测仪比较cpDNA浓度和纯度。通过叶绿体全基因组序列比对，基因重排检测及基因富集分析，分析直接测序与参考拼接测序两种测序方法的差异，为梅叶绿体提取及测序提供参考。通过叶绿体基因组测序，系统进化树构建，从叶绿体基因组角度解释李属植物进化关系，分析叶绿体基因组简单重复序列信息区分梅，李，杏三物种，进而进行SSR分子标记的开发，为叶绿体基因组的研究及李属的系统发育，种质鉴定及遗传群体分析提供参考。主要研究结果如下： 1. 通过比较改良高盐-低pH法，叶绿体试剂盒，高盐-低pH配合Percoll密度梯度法分离叶绿体，并提取梅品种“龙眼”中叶绿体DNA。结果表明，采用改良高盐-低pH法能够获得完整的叶绿体及高浓度和高纯度的叶绿体DNA，是最适合梅的叶绿体分离的方法。叶绿体全基因组序列比对、基因重排检测以及基因富集分析显示直接测序法与参考拼接测序法的明显差异为IR区的一段冗余序列。两者基因组重排相似度高于99%。 2.以梅品种‘龙眼’，杏品种‘金太阳’，李品种‘盖县大李’为材料进行高通量测序得到三者完整的叶绿体基因组序列。比较基因组分析发现trnY-ATA为杏的特有基因，trnI-TAT在梅李上排列顺序不一样，且为两物种特有。叶绿体全基因序列对比发现17个差异热点区域，与SSR的分布正相关。系统进化分析从叶绿体基因组的角度证明与李相比，梅与杏的遗传关系更为密切。 3.利用梅杏李三个物种叶绿体基因组数据分析设计了162对引物，通过丙烯酰胺凝胶电泳的方法检测了60份李属植物的DNA扩增产物的多态性。通过进一步筛选，筛选出两对SSR引物，它们具有物种特异扩增片段，可从物种水平区分梅，杏，李以及三者遗传群体分析，还可用于种质鉴定和遗传多样性分析。

Prunus mume, Prunus armeniaca and Prunus salicina are important fruit trees in China are important fruit trees in China. They can not only be used as fresh food, but also process fruit wine and candied fruit, which is of great economic and research value. Chloroplast genome has the characteristics of small size, cytoplasmic inheritance, low nucleotides replacement rate, haploid property and highly conserved genome structure, which is an ideal genome for thestudy of plant breeding, phylogeny and geographical domestication. In this study, chloroplast separation was compared by plant chloroplast DNA kit, high salt-low pH combined with Percoll density gradient and improved high salt-low pH method. The chloroplast integrity was detected by fluorescence microscope examination. The concentration and purity of cpDNA was detected by agarose gel electrophoresis and nucleic acid detector. Through complete chloroplas genome sequence alignment, gene rearrangement detection and gene enrichment analysis, the differences between direct sequencing and reference sequencing were analyzed to provide reference for the extraction and sequencing in Prunus Mume. Through chloroplast genome sequencing and systematic evolution tree construction, the evolutionary relationship of Prunus genus was explained from the perspective of chloroplast genome, and the simple repetitive sequence information of chloroplast genome was analyzed to distinguish Prunus mume, Prunus armeniaca and Prunus salicina. Furthermore, the development of SSR molecular markers provided a reference for the study of chloroplast genome and the phylogeny, germplasm identification and genetic population analysis of the Prunus genus. The main findings are as follows: 1.The effect of chloroplast separation was compared by improved high salt-low pH method, plant chloroplast DNA kit, high salt-low pH combined with Percoll density gradient method, and chloroplast DNA of Prunus mume variety “Longyan” was extracted. The results showed that complete chloroplast and high concentration and high puritychloroplast DNA could be obtained by improved high salt-low pH method, which was the most suitable method for chloroplast separation of Prunus mume. Chloroplast genome sequence alignment, gene rearrangement detection and gene enrichment analysis showed that the significant difference between direct sequencing method and reference splicing sequencing method was a redundant sequence in IR region. The similarity of genome rearrangement was higher than 99%. 2.The chloroplast genome sequences of Prunus mume variety “longyan”, Prunus armeniaca variety “Jintaiyang” and Prunus salicina variety “Gaixian Dali” were obtained by high throughput sequencing. Genome analysis showed that trnY-ATA was a specific gene of Prunus armeniaca, trnI-TAT was not arranged in the same order on Prunus mume and Prunus salicina and it was specific to the two species. Comparison of chloroplast complete gene sequence showed that 17 different regions were positively correlated with the distribution of SSR. From the point of view of chloroplast genome, systematic evolution analysis proved that Prunus armeniaca and Prunus salicina were more closely related to each other than Prunus mume. 3.We designed 162 pairs of primers from the chloroplast fenome of three Prunus genus plant, the DNA amplification and polymorphism of 60 Prunus genus plants were detected by PAGE gel analysis. And two SSR primer pairs were screened out with clear polymorphic markers which could be used not only in the genetic population analysis but also in germplasm identification and a genetic diversity analysis.