稻属中转座子插入基因的式样及适应性进化研究
樊亚宇
学位类型硕士
导师高立志
2010-05
学位授予单位中国科学院研究生院
学位专业植物学
摘要转座子在各类真核生物基因组中都占有很高的比例,它们对基因组及宿主基因结构、功能和进化都有重要作用。目前已有很多研究在探讨转座子对于其宿主基因及基因组的贡献,但是迄今对于转座子在基因组中的插入式样及保留机制,以及转座子对于基因及基因组适应性进化方面的影响等问题仍然没有透彻的认识。基于对整个水稻基因组的生物信息学分析,本研究报道了水稻基因组17个转座子在稻属16个种中在转座子插入基因中的插入式样;检测了转座子插入事件发生前后插入位点周围区域的序列多态性及进化模式;讨论了稻属AA基因组基部类群种间进化关系。主要研究结果如下:对于每一个转座子插入基因,在94份稻属材料中进行PCR扩增,电泳分析,得到17个转座子在稻属物种中的插入式样。我们发现,不同的转座子在稻属诸种的分布范围不同,其中2个转座子在稻属所有的材料中都有插入;其余15个转座子只在部分种中存在。根据不同转座子的插入式样我们推断,本研究所选转座子插入事件主要发生在AA基因组分化前后,并且插入在AA基因组的祖先种中,随着AA基因组的继续分化而分布在各个种中;同时,根据转座子插入时间,我们验证了稻属AA基因组中最早分化出来的种为Oryza meridionalis 而非O. longistaminata。对于一部分在祖先群体中固定下来的转座子,我们对转座子插入事件前后群体中插入位点区域进行了核苷酸多态性分析及中性检测,并没有得到显著结果。因此,插入突变在祖先种群体中的固定可能并没有受到选择作用,而是一个中性突变随机积累的过程,但是不排除由于插入事件发生较早,固定过程已经完成,因此无法从序列水平上检测出来的可能性
资助项目Transposable elements (TEs) have been found to be a significant fraction of eukaryotic genomes. Moreover, they make great contributions to the structure, function and evolution of genomes as well as genes. However, some questions such as the mechanisms of retainment of TEs in the genome and their adaptive evolution have not been fully elucidated so far. In this study, the distributions of 17 TE-gene associations among Oryza species were investigated. In addition, the nucleotide diversity was analysed and neutral tests for the region flanking the TE insertions were performed. Based on the above-observed patterns, evolutionary relationships between species in the AA genome group were discussed. The main results are as follows: For each TE-gene association, PCR and electrophoresis were conducted for a total of 107 strains, belonging to different Oryza species. The patterns of each TE-gene association in different species were obtained. It is our finding that 2 associations distribute through all Oryza species. By contrast, other 15 associations were only observed in some Oryza species. On basis of the above-mentioned results, it is likely that insertion events under study occurred in their common ancestor, and then they dispersed with subsequent divergence of different AA genome species. Our datas strongly support that O. meridionalis is the most basal lineage of AA genome group, instead of O. longistaminata.For several TE-gene associations fixed in populations of ancestor, the nucleotide diversity was estimated and neutral tests for the region flanking the TE insertions between populations with and without TE insertions were performed. No significant result was obtained. It is possible that the fixation of mutations with TE insetion is a random process; alternatively, this process is attributable to nature selection. Since the fixation has finished, it is difficult to detect the signature at the sequence level.
语种中文
文献类型学位论文
条目标识符http://ir.kib.ac.cn/handle/151853/16194
专题昆明植物所硕博研究生毕业学位论文
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樊亚宇. 稻属中转座子插入基因的式样及适应性进化研究[D]. 中国科学院研究生院,2010.
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