| 题名 | 黑胫病菌基因组的组装与比较基因组学分析兼论生物信息软件的开发与应用 |
| 作者 | 刘晖 |
| 学位类别 | 博士 |
| 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 | 王文 |
| 关键词 | 黑胫病菌 基因组 PacBio SNP注释 假染色体组装 |
| 其他题名 | Genome assembly and comparative analysis of Phytophthora nicotianae and development of bioinformatic |
| 中文摘要 | 黑胫病对植物危害严重，植物感染后会茎部发黑、枯萎并迅速死亡，其致病因子是一种半活体营养型的土壤生卵菌——黑胫病菌。烟草黑胫病是研究黑胫病致病机理的重要模型。烟草黑胫病菌存在两个侵染性十分不同的生理小种，分别称为0号和1号。在以中高度抗性的烟草植株为对象的研究中发现，0号侵袭力较强，潜伏期短，根腐症状严重，而1号造成的萎缩症状更为严重。本论文的研究工作使用PacBio单分子实时测序技术（PacBio SMRT Sequencing）和传统二代测序技术（Second Generation Sequencing，SGS），对黑胫病菌的两个生理小种（0号、1号）进行了基因组测序组装与数据挖掘。通过比较基因组学分析，发现一个枯萎诱导（Necrosis Inducing）蛋白在0号、1号生理小种之间受到正选择，并在1号生理小种上发生了氨基酸丢失，这可能与不同生理小种间的侵袭力（aggressiveness）差异有关；发现一个ABC运输蛋白家族发生了扩张，ABC蛋白与病原菌的感染密切相关，该蛋白家族的扩张可能与黑胫病菌的宿主适应性有关。 本人博士论文的另一部分研究内容是生物信息软件的开发与应用。随着测序技术的不断发展及科学研究的不断深入，如何从爆炸式增加的海量数据中挖掘有效生物信息是摆在所有生物学家面前的难题。虽然生物信息分析软件越来越多，但面对实际应用时仍需要很多研发。本论文开发了两款软件，分别是AnnoSNP和XFanchor。AnnoSNP调用了BioPerl，功能是对SNP注释，预测其对基因的突变影响；XFanchor使用了动态编程技术，基于近缘参考基因组将组装好的contig进行假染色体组装。这些软件在对本人所在实验室的绢丝昆虫转录组、水稻重测序、野生稻基因组、石斛基因组等生物信息挖掘时起到了重要的作用。 |
| 英文摘要 | Black shank is one of the most destructive plant diseases. Infected plant will ex-hibit syndromes like blackened stems, root rot, necrosis and die soon. The casual agent is a kind of soil-born heimi-biotrophic pathogen - Phytophthora nicotianae. In compatible studies between P. nicotianae and tobacco cultivars with moderate and high levels of partial resistance, race 0 was more aggressive, the incubation periods was shorter and the severity of root rot it caused was greater. And race 1 isolate caused greater stunting. By using Third Generation Sequencing (TGS) and Second Generation Sequencing (SGS), we sequenced and assembled the genomes of two rac-es of Phytophthora nicotianae, race 0 and race 1. Through comparative genomic analysis, we identified a Necrosis Inducing Protein positively selected between race 0 and race 1, and we found a deletion of 7 amino acids of this gene in the race 1, which may contribute to the aggressiveness difference between race 0 and race 1. We also found one ABC transporter protein gene family expanded in the lineage of Phy-tophthora nicotianae, compared with its close relative Phytophthora infestans. This expansion may be a result of adaption of Phytophthora nicotianae to hosts like citrus and tobacco. Another part of this thesis is developing bioinformatic tools. As the development of DNA sequencing techniques, how to efficiently mining biological information from explosive increasing omics data has become an urgent task. Though lots of analytic tools have been developed, more and more softwares targeting different kinds of data are still needed in bioinformatics practice. We developed two programs to deal with practical problems caused by different materials and different aims: AnnoSNP and XFanchor. AnnoSNP used modules from BioPerl and was developed to predict the effect of SNPs on corresponding coding genes. XFanchor used dynamic programming to anchor assembled contigs to chromosomes based on a closely related reference. These programs played important roles in analyses of transcriptomes of silkmoths, rice resequencing, genome of Oryza longistaminata and genome of Dendrobium officinale in my host laboratory. |
| 语种 | 中文 |
| 内容类型 | 学位论文 |
| 源URL | [http://159.226.149.26:8080/handle/152453/10182]  |
| 专题 | 昆明动物研究所_基因起源组 |
| 推荐引用方式 GB/T 7714 | 刘晖. 黑胫病菌基因组的组装与比较基因组学分析兼论生物信息软件的开发与应用[D]. 北京. 中国科学院研究生院. 2015. |
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