酵母、眼镜蛇和绵羊的基因组与转录组分析
文献类型：学位论文
| 作者 | 姜雨 |
| 学位类别 | 博士 |
| 答辩日期 | 2011-05 |
| 授予单位 | 中国科学院研究生院 |
| 授予地点 | 北京 |
| 导师 | 王文 |
| 关键词 | 酿酒酵母 基因渗入 从头起源 眼镜蛇 三指毒素 绵羊 基因组 |
| 其他题名 | Genomics and Transcriptomes Analysis of Yeasts, Elapids and Sheep |
| 学位专业 | 遗传学 |
| 中文摘要 | 本论文对酵母、眼镜蛇和绵羊三种不同类型的真核生物进行基因组和转录组水平的进化功能分析，在序列水平系统研究这些物种的特性。 首先，我们对最先获得基因组和群体数据的真核生物——酿酒酵母的物种起源历史和进化过程出现的新基因进行了深入研究。通过对73个世界各地的酵母菌株进行全基因组筛查，我们找到四十多个酿酒酵母和它的近缘种奇异酵母之间的基因渗入片段，结合这些酵母品系的地理分布，我们得出结论：世界各地的酿酒酵母都起源于欧洲；同时也提出基因转移事件是一个非常好的可以用于研究各类生物的地理起源的分子遗传标记。同时，我们对酿酒酵母和其近缘物种的基因组进行同源比较，在酿酒酵母中找到了数十个由基因重复产生的和两个从头起源的新基因。 其次，眼镜蛇科的毒蛇拥有世界上最毒的毒液，蛇毒素基因也是自然界中进化最迅速的基因之一。我们首次测序了眼镜蛇科在旧大陆分布最广泛的两种毒蛇——银环蛇和眼镜蛇的毒腺转录谱，并构建了这两种毒蛇的基因组BAC文库，在全基因组水平筛选出其中包含有最主要毒素基因家族的阳性BAC克隆，并测序了检测得到的全部三指毒素基因（3FTx）。这使得我们对眼镜蛇科的毒素谱型有了进一步的了解，并认识到3FTx基因家族成员主要是通过大量的串联重复形成的。 随着新一代测序技术和配套研究的成熟，家养动物大基因组的短片段测序、组装和分析研究变得可行。我们首次测序、组装出了绵羊的参考基因组，Scaffold N50达到了1.1Mb，95%的基因组序列被装配到了染色体上，并通过七种组织的转录组测序，辅助注释出了两万多个基因。多种质量控制证明这是一个组装得非常好的基因组。通过进化基因组学比较，我们建立了反刍动物的同源基因数据库，并对绵羊的高山生活适应性和经济性状进行分析研究。 |
| 英文摘要 | In this dissertation, we systematically studied the evolutionary patterns of yeasts, elapid snakes and sheep at the genomic and transcriptomic level. The budding yeast（Saccharomyces cerevisiae）is the first completely sequenced eukaryote and the genomic sequences of its relative species or strains were also available available during the last decade. We identified about 40 introgression segments between S. cerevisiae and its sibling species S. paradoxus, by screening the nuclear-sequence data from 73 globally distributed natural and domesticated yeast populations. As new useful genetic markers, the gene flow events indicate S. cerevisiae was originated from Europe and expend to other continents after S. paradoxus had been a global microbe. We identified dozens of new duplicated genes and two de novo originated genes in S. cerevisiae. Kraits and cobras are two representative toxic genera of elapids in the old world. To unveil their detailed venoms and their evolutionary patterns, we constructed venom gland cDNA libraries and genomic bacterial artificial chromosome（BAC） libraries for Bungarus multicinctus and Naja atra, respectively. We sequenced the venom transcriptomes and screened the BAC libraries of the two snakes by blot analysis. Based on the toxin ESTs and the three finger toxin（3FTx）gene sequences, the major components of the two venom transcriptomes were well known. The data also revealed that tandem duplications contributed the most to the expansion of toxin multigene families. Thanks to the use of next-generation sequencing tools, the big genome of domesticated animals become more easily available. We finished the sequencing, de novo assembly and annotation of the draft reference sheep（Ovis aries）genome. The N50 length of the assembled scaffolds is 1.1Mb, and the scaffold sets achieve a total length of 2.71 Gb, which covers approximately 91% of the whole sheep genome. Using both the male and female Texel sequence, we separately identified about 5 million heterozygous single nucleotide polymorphisms. Seven tissue samples derived from the same Texel ewe were used for Illumina mRNA-seq to define the expressed portion of the genome. Through comparative genomic analysis, we have built the ruminant orthology database, and analysed the adaptability in mountainous areas and the economic characters for sheep. |
| 语种 | 中文 |
| 公开日期 | 2011-09-19 |
| 源URL | [http://159.226.149.42:8088/handle/353002/6789]  |
| 专题 | 昆明动物研究所_基因起源组 |
| 推荐引用方式 GB/T 7714 | 姜雨. 酵母、眼镜蛇和绵羊的基因组与转录组分析[D]. 北京. 中国科学院研究生院. 2011. |
入库方式： OAI收割
来源：昆明动物研究所
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