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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2010 [1]

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Funding Project：Bambusoideae belongs to BEP clade of Poaceae. Bambusoideae in general, and Arundinarieae in particular, has long been considered a complex and taxonomically difficult group. In this study, six bamboo chloroplast genomes were sequenced. One of the six bamboos belongs to Bamabuseae (Bambusa emeiensis) and the other five belong to Arundinarieae (Ferrocalamus rimosivaginus, Acidosasa purpurea, Indocalamus longiauritus, Phyllostachys edulis and Phyllostachys nigra var. henonis). It was a first attempt to address phylogenetic issue in Bambusoideae using phylogenomics. The aim of the thesis is to resolve the relationships of five species in Arundinarieae and to evaluate the efficiency of phylogenomic strategy in bamboo phylogenetic study. Through comparing eight bamboo chloroplast genomes, we were able to identify fast-involving fragments for further phylogenetic studies in Bambusoideae. The main results were summarized as follows: 1. The complete sequences of six bamboo chloroplast genomes have verified the feasibility and reliability of using the next-generation platform to sequencing the chloroplast genomes isolated through improved method of high ionic strength in combination with low pH buffer. Comparative studies indicated that eight chloroplast genomes of Bambusoideae which encoded an identical set of genes were rather conserved and perfectly syntenic. We identified repeat sequences of the six newly sequenced bamboo chloroplast genomes and coded these repeat sequences as whole genome features according to their distributions in six chloroplast genomes. The coded matrix was used for construction of phylogenetic tree using maximum parsimony analysis. The result provided strong support for the position of F. rimosivaginus as the earliest diverging species of the five bamboos in Arundinarieae, followed by A. purpurea, I. longiauritus and a clade consisted of P. edulis and P. nigra var. henonis. 2. Phylogenetic studies based on twenty-four complete chloroplast genomes of Poaceae provided a strong support for the sister relationship between Bambusoideae and Pooideae within BEP clade. Within Arundinarieae, I. longiauritus, P. edulis and P. nigra var. henonis were proved to be a monophyletic clade (referred as Phyllostachys clade) in which P. edulis and P. nigra var. henonis had a closer relationship. A. purpurea was siter to Phyllostachys clade. However, this relationship was only supported by Bayesian analysis. This result was considered reasonable while combining with the phylogenetic result based on whole genome features. Phylogenetic analyses were performed based on the following data partitions: (1) the complete chloroplast genome sequences, (2) a set of 74 common protein-coding genes, (3) the large single copy region, and (4) the small single copy region. The result from the complete chloroplast DNA sequence was proved to be better than results from other three data partitions. Unambiguously possibly informative exon indels were identified and mapped to chloroplast genome-based phylogenetic tree. Of the forty-five indels, twenty-five mapped to monophyletic groups, therefore they may be synapomorphies. The remainder of these events may be homoplasies resulted from parallel evolution or back mutation. Forty-five indels were coded and added to the protein-coding gene matrix. Then the matrix was used for phylogenetic analysis and the result indicated that these coded indels did not change the tree topology, while the bootstrap values of some nodes were increased. In conclusion, it was proved to be efficient to reconstruct bamboo phylogeny using chloroplast phylogenomics. 3. The number and distribution pattern of variable characters in each homologous region were rather different in three subfamilies. Therefore, it is more reasonable to select fast-evolving regions from bamboo chloroplast genomes. The average proportion of variability in noncoding regions was as twice as in the coding regions. Therefore, we identified twenty fast-involving markers from noncoding regions.

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