题名 | 家养动物线粒体DNA系统发育基因组学研究 |
作者 | 史妮妮 |
学位类别 | 硕士 |
答辩日期 | 2015-05 |
授予单位 | 中国科学院研究生院 |
授予地点 | 北京 |
导师 | 张亚平 |
关键词 | 线粒体DNA 家养动物 mtDNA单倍型类群树 系统发育 家鸡驯化 |
其他题名 | Mitochondrial DNA Phylogenomics in Domestic Animals |
学位专业 | 生物工程 |
中文摘要 | 线粒体DNA(mitochondrial DNA,mtDNA)是位于细胞器线粒体内的双链环状DNA分子。在脊椎动物中,mtDNA遵循母系遗传,缺乏重组的遗传模式。相比核DNA(nuclear DNA),mtDNA具有较高的进化速率。正是由于这些的遗传特性,mtDNA已经成为重建家养动物群体历史的分子标记。基于mtDNA全基因组数据构建家养动物的系统发育关系(phylogeny)——系统发育基因组学(phylogenomics)为深入探讨其起源与驯化历史提供了坚实的基础。本文将围绕mtDNA系统发育关系构建及其运用,开展关于家养动物mtDNA基因组学研究。 在第一章,我们介绍了家养动物mtDNA研究的概况及相关进展,第二章中,我们首先对收集到的mtDNA基因组数据质量进行了系统的评估,发现194条序列存在质量问题(人为重组,突变过多和幻影突变)。然后基于目前已有的mtDNA基因组数据,我们手工构建了8种家养动物(家犬,家牛,牦牛,家猪,家马,家鸡,山羊和绵羊)的mtDNA单倍型类群树(haplogroup tree)。在此基础上,我们更新了8种家养动物的mtDNA世系(lineage)系统发育关系和命名系统,并开发了相应的网页数据库DomeTree(http://www.dometree.org/)以及数据分析软件MitoToolPy(http://www.mitotool.org/mp.html)。在第三章,我们参照家鸡的mtDNA单倍型类群树重新分析了4938条家鸡mtDNA序列数据发现单倍型类群C1是追溯中国北方(特别是黄淮流域)家鸡驯化的一个候选标记。 |
英文摘要 | Mitochondrial DNA (mtDNA), as a double stranded and circular DNA molecule, is located in the mitochondria. In vertebrates, mtDNA lacks of recombination and follows matrilineal inheritance. The mutation rate of mtDNA is higher than those of nuclear DNA (nuclear DNA). Due to these unique features, mtDNA serves as a powerful tool in tracing the history of domesticated animal. Based on mtDNA genome data to construct phylogeny phylogenomic analyses can provide more details for the origin and domestication for domesticated animals. This thesis will revolve around this stategy to conduct mtDNA genomics researches for the domesticated animals. In the first chapter, we introduced the development and progress in the mtDNA studies of domesticated animals’ mtDNA genomics and the phylogenomics, as background knowledge for the phylogeny reconstruction of domesticated animals. In the second chapter, First of all, we carried on the system of evaluation for all mtDNA genome data quality and we found that the 194 series quality problems (artificial restructuring, surplus of mutation and phantom mutations). Then we manually construct haplogroup tree for 8 kinds of domesticated animals based on the currently existing mtDNA genome data. Finally, according to the updated mtDNA haplogroup tree, we conduct data analysis of the domesticated animals mtDNA genome and develop the bioinformatics software MitoToolPy (http://www.mitotool.org/mp.html). In the third chapter, referring to the updated chickens mtDNA haplogroup tree, we analyse phylogenetic relationship and genetic diversity analysis for 4938 chickens of mtDNA data, we confirmed that the northern China, especially in huanghuai river basin might be another acclimatization center of chickens. |
语种 | 中文 |
内容类型 | 学位论文 |
源URL | [http://159.226.149.26:8080/handle/152453/10202] |
专题 | 昆明动物研究所_分子进化基因组学 |
推荐引用方式 GB/T 7714 | 史妮妮. 家养动物线粒体DNA系统发育基因组学研究[D]. 北京. 中国科学院研究生院. 2015. |
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