中国科学院昆明植物研究所知识管理系统(KIB OpenIR): Search Results

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Community：昆明植物所硕博研究生毕业学位论文 First author affiliation The first author Corresponding Author Funding Project：C. sinensis var. assamica is an important member of section Thea, belonging to the genus Camellia. It becomes more and more attractive because of its medicine and health maintenance efficacy. The chloroplast genome sequence is now widely used to resolve the phylogeny at different levels of taxonomic categories, because of its small genome size and different evolutionary rates of coding and noncoding gene regions. Futhermore with the progression in chloroplast genetic engineering, we can improve the quantity and quality of crops efficiently. However, the isolation of high yield and purified chloroplast DNA of Camellia becomes very difficult due to special leaf structure and complicated metabolic products. Unfortunately there are not any efficient methods available to isolate the Camellia cpDNA. In this study, we established an efficient method to isolate the Camellia cpDNA on basis of its leaf structure and complicate compounds. With the purified and sufficient cpDNAs, we completed sequencing the first chloroplast genome in the Genus Camellia, even the first one in the order Ericales. Besides, we used the information of genomic rearrangement of chloroplast to reconstruction the phylogenetic relationship of the three basal algal groups to investigate the feasibility of using genomic rearrangement for phylogeny reconstruction. Results are as below: 1. Isolation of cpDNAs of Section Thea of the genus Camellia, Based on special leaf structure and components of Section Thea of the genus Camellia, we adjusted experimental conditions and established a suitable protocol for its chloroplast isolation. They included short time and high speed homogenate, combined with a low pH extraction buffer for cell breakage, differential centrifugation for isolating the chloroplasts, high-salt wash buffers for the elimination of nuclear DNA contamination and phenol-chloroform treatment. As a result, sufficiently purified and successfully digested cpDNAs was abtained. They can be directly sequenced by Solexa. 2. Complete chloroplast genome sequence of C. sinensis var. assamica, With the second generation sequencing technology of Solexa, we completed the first chloroplast genome sequencing of the genus Camellia, also the first one of order Ericales. The genome size is 157,140bp, and the lengths of LSC, SSC, IR are 86,600bp, 18,272bp, 26,134bp, respectively. The genome contains 115 genes, including 30 tRNA genes and 4 rRNA genes. Futhermore, with the complete cpDNA of C. sinensis var.assamica and other completely sequenced cpDNAs of Asterids, we compared shade-loving and sun plants, the chloroplast structures of the two kinds of plants are very similar, but we found that nucleotide substitution rates of shade-loving plants are lower than sun plants. A likely explanation is that more variations accumulated by more chloroplasts in cells of sun plants. 3. Feasibility to use genomic rearrangement for the phylogeny reconstruction: a case study on the phylogeny reconstruction of basal alagal groups, Phylogeny of three basal algal groups, glaucophyta, chlorophyta and rhodophyta, was first reconstructed by means of rearrangement information from the chloroplast genomes. It includes common genes content, conserved gene clusters and phylogenetic trees produced by gene order data. We found that glaucophyta and rhodophyta share more common genes, and the conserved gene clusters between them have fewer arrangements. Furthermore phylogenetic trees also showed closer relationships between glaucophyta and rhodophyta. Thus our results supported that chlorophyta are sister to glaucophyta plus rhodophyta.

中国科学院昆明植物研究所知识管理系统

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