基于叶绿体全基因组的竹子系统发育基因组学研究
张韵洁
学位类型硕士
导师李德铢
2010-11
学位授予单位中国科学院研究生院
学位专业植物学
摘要竹亚科属于禾本科BEP分支,约包含1000-1500个种。竹亚科,特别是温带木本竹子分支一直是系统发育研究的难点。本研究对竹亚科热带分支的慈竹 (Bambusa emeiensis),温带分支的裂箨铁竹(Ferrocalamus rimosivaginus)、毛花酸竹(Acidosasa purpurea)、箬叶竹 (Indocalamus longiauritus)、毛竹 (Phyllostachys edulis) 和毛金竹 (Phyllostachys nigra var. henonis) 共六种竹子的叶绿体全基因组进行了测序。首次尝试以系统发育基因组学手段,对竹亚科系统发育关系进行重建,以期解决温带分支内部的系统发育关系,并探讨系统发育基因组学手段用于竹亚科系统发育重建的可行性。同时,结合已发表的两种竹子叶绿体基因组,在全叶绿体基因组水平上筛选了一些分子进化速率相对较快的片段,以期望能用于竹亚科分子系统学研究。主要研究结果如下:1. 六种竹子叶绿体基因组的测序结果,证实了通过改良高盐低pH法直接分离叶绿体基因组,并采用新一代测序技术进行测序这一方法的可行性及可靠性。通过八种竹子叶绿体全基因组序列比对发现,竹亚科植物的叶绿体基因组非常保守,具有良好的共线性,编码一套相同的基因。根据重复序列在各个基因组中的共有方式进行编码,以最大简约法对六种竹子的系统发育关系进行初步分析,结果表明温带分支中裂箨铁竹最先分异,其次依次是毛花酸竹、箬叶竹、毛竹和毛金竹。2. 以禾本科24个全叶绿体基因组序列进行的系统发育重建结果,证实了BEP分支中早熟禾亚科与竹亚科为姊妹关系。温带分支的系统发育结果支持毛竹与毛金竹构成单系,并与箬叶竹聚为一支。毛花酸竹与[箬叶竹+(毛竹+毛金竹)]聚为一支,但这一关系仅得到贝叶斯分析的支持,结合以重复序列为代表的基因组特征分析结果,认为这一关系较为合理。对全叶绿体基因组序列、74个基因编码区序列、大单拷贝区序列、小单拷贝区序列四组数据分别进行系统发育分析,结果表明基于全叶绿体基因组序列的系统发育分析结果较为理想。对基因中插入缺失的研究发现,45个插入/缺失中有25个可能为共近裔性状,20个可能为同塑性性状。将这45个插入缺失进行编码,加入编码基因序列矩阵进行分析,结果对原系统树的拓扑结构并无影响,但某些分支的支持率有所提高。综合以上结果表明,采用叶绿体系统发育基因组学手段对竹亚科植物进行系统发育重建是较为有效的方法。3. 叶绿体基因组中变异位点的数目及分布方式在三个亚科之间存在差异,因此基于八种竹子的叶绿体基因组进行分子标记的筛选更为合理。竹亚科植物叶绿体基因组的非编码区变异率较快,平均变异率约为编码区的两倍,因此本研究主要从非编码区中筛选了20个变异速率较快的分子片段。
资助项目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.
语种中文
文献类型学位论文
条目标识符http://ir.kib.ac.cn/handle/151853/16112
专题昆明植物所硕博研究生毕业学位论文
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张韵洁. 基于叶绿体全基因组的竹子系统发育基因组学研究[D]. 中国科学院研究生院,2010.
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