结合Illumina和PacBio SMRT测序技术对复杂植物基因组组装方法的探究
文献类型：学位论文
| 作者 | 王筱 |
| 学位类别 | 硕士 |
| 答辩日期 | 2015-04 |
| 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 | 复杂基因组 基因组组装 Illumina Hiseq测序 PacBio测序 实时单分子 铁皮石斛 |
| 其他题名 | The exploration of complex plant genome assembly method combining with Illumina & PacBio SMRT sequen |
| 学位专业 | 生物工程 |
| 中文摘要 | 自1977年第一代sanger测序技术发展至今，已有四十多年时间，测序技术快速发展和变革，极大推动了生物领域及医学领域的快速发展。Sanger测序技术读长长，准确性高，但测序成本高，通量低，影响了其大规模应用。以Illumina公司的Hiseq技术为代表的二代技术的出现，大大降低了测序成本，在保证高准确性的同时大幅提高了测序速度，完成了多种动植物的基因组de novo组装。在复杂植物基因组中，往往存在高杂合、高重复等特点，而Hiseq Illumina测序技术并不能完全避免GC含量的影响，使得复杂基因组完整组装分析遇到巨大障碍。随着第三代实时单分子测序技术的开发，长度长的特性以及免去GC偏好型的特征，使其在基因组组装及相关挖掘方面产生巨大推进作用。本文以铁皮石斛和丹参为例，探讨了结合低覆盖度的PacBio SMRT数据对基因组de novo组装完整度的提升。我们与吉林大学严亮博士合作，从技术角度探索了铁皮石斛复杂基因组的解析方法，得到contigN50=25.1kb，scaffoldN50 = 76.4kb的基因组草图，测序量合计覆盖超过了铁皮石斛基因组94%的序列，大约97.56%的蛋白质编码基因被功能注释。同时，我们与昆明理工大学董扬教授合作，通过结合二代、三代测序方法，得到contigN50=82.8kb，scaffoldN50 = 122.4kb的丹参基因组草图。通过铁皮石斛和丹参复杂基因组组装分析，本文归纳出了一种完整的基于二代、三代基因组测序技术针对高杂合、高重复基因组的组装方法，显示出第三代测序技术在大型复杂基因组de novo组装中的应用前景。 |
| 英文摘要 | Since 1977, the first generation of sanger sequencing technology has been developmented for more than 40 years, the rapid development and revolution sequencing technology has also greatly accelerated biological and biomedical research dramatically. Sanger sequencing technology has the feature of read long and high accuracy, but the high cost and low flux affected its large-scale application. In the last few years, with the wide spread of the second generation sequencing technology which represented by the Illumina Hiseq technology,the cost of sequencing was greatly reduced and the high accuracy were also guaranteed at the same time. The de novo assembly of a variety of animal and plant genomes were proceeded. However, in complex plant genomes, it tend to have high heterozygosity and high repetition, and Hiseq Illumina sequencing technology cannot completely avoid the influence of GC content, making the analysis of complete genome assembly encountered great obstacles. The 3rd generation, SMRT sequencing technology, overcome the GC bias, long in read length, will lead great improvement in complex genome assembly. Here we take the Dendrobium officinale Kimura et for example, in collaboration with Dr. Liang Yan, combining with the second generation of Illumina HiSeq 2000 sequencing technology and the third generation of PacBio sequencing technology, from the point of view of technology to explore the Dendrobium officinale complex genome analysis method. Finally we get the draft genome with contigN50 = 25.1 kb,scaffoldN50 = 76.4 kb, the total amount of sequencing covers more than 94% of dendrobium genome sequence, the function annotates 97.56% of D. officinale protein-coding genes. Meanwhile, we also get the dra ft genome of Salvia miltiorrhiza with contigN50 = 82.8 kb, scaffoldN50 = 122.4 kb. By analyzing D. officinale complex genome assembly, this paper summarized a method for complex genome assembly based on second generation and third generation sequencing technology, which also shows the application prospect of the third generation sequencing technology in large complex genome assembly. |
| 语种 | 中文 |
| 源URL | [http://159.226.149.26:8080/handle/152453/10197]  |
| 专题 | 昆明动物研究所_基因起源组 |
| 推荐引用方式 GB/T 7714 | 王筱. 结合Illumina和PacBio SMRT测序技术对复杂植物基因组组装方法的探究[D]. 北京. 中国科学院研究生院. 2015. |
入库方式： OAI收割
来源：昆明动物研究所
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