棉花功能基因组学平台构建和非编码转录组学数据挖掘

发布时间：2018-04-15 10:04

  本文选题：棉花 + 功能基因组学平台　； 参考：《中国农业大学》2016年博士论文

【摘要】：棉花是重要的纤维及油料作物之一,包括50余个不同的棉种。其中陆地棉是主要栽培种之一,是由雷蒙德氏棉(D基因组)和亚洲棉(A基因组)两个二倍体棉种自然杂交后进化形成的。由高盐和干旱等环境因素引起的水分胁迫,是制约棉花生产的主要因素之一。对雷蒙德氏棉和亚洲棉的功能基因组学研究,将有助于陆地棉生产和抗逆能力的改良。本文通过生物信息学方法构建了雷蒙德氏棉功能基因组学平台,利用小RNA测序和降解组测序手段对亚洲棉根组织响应盐胁迫的miRNA及其靶基因进行了鉴定,通过对靶基因的功能富集分析和miRNA双色调控网络分析,我对miRNA参与盐胁迫响应的功能进行了研究。同时,我还对亚洲棉响应水分胁迫的siRNA位点进行了初步探索。雷蒙德氏棉是首个完成基因组测序的棉种。我比较了两个不同版本(JGI和BGI)基因组序列的差异,并从中挑选了JGI版本基因组数据。以信号转导、转录调控、次生代谢、分子转运等途径为核心,进行了相关基因家族的分类。利用近缘物种的生物学知识,我构建了蛋白-蛋白互作网络,并对其进行了模块化分析和功能注释,找到了91个与胁迫响应、信号转导、转录调控、次生代谢相关的网络模块。我还对已有的miRNA进行了整合,并预测了下游的靶基因。对基因的基本功能进行了注释,包括GO、KEGG、MapMan、保守功能结构域和启动子附近的顺式作用元件等。基于这些结果,我构建了功能基因组学平台(GraP:http://structuralbiology.cau.edu.cn/GraP/并提供了多种查询检索工具。同时,我还为用户提供了顺式作用元件和基因功能富集分析工具,以满足用户的分析需求。亚洲棉具有良好的遗传稳定性和胁迫耐受性。根是植物吸收营养、合成激素、感受胁迫等的重要器官,其中miRNA可能参与了对胁迫响应、根发育的调控。我用小RNA测序和降解组学技术,在盐胁迫条件下对亚洲棉根组织的miRNA及其靶基因进行了研究。通过niRNA-seq差异表达分析找到了84个响应盐胁迫的miRNA,对部分miRNA进行了qRT-PC R验证。同时,还利用降解组学方法对miRNA靶基因进行了验证。对靶基因进行GO富集分析,我发现miRNA在胁迫条件下的变化可能加速棉花从营养生长向生殖生长的转变,致使棉花早熟以促进其对胁迫的逃逸性。此外,我构建了miRNA双色调控网络,并对网络模块进行了功能挖掘,发现miRNA可能间接参与了激素相关次生代谢、激素信号转导和(非)生物胁迫之间互作的调控。另外,siRNA可以介导DNA甲基化,在表观遗传水平参与胁迫响应的调控。我运用实验室前期产生的数据,对亚洲棉响应水分胁迫的siRNA位点进行了鉴定,根据siRNA位点、DNA重复元件和基因的位置关系,筛选了与胁迫响应siRNA相关的差异表达基因。我对这些基因进行GO分析,发现上调的siRNA相关基因主要参与了胁迫响应、信号转导和转录调控等过程,而下调基因主要参与生物分子的转运过程。本研究构建了棉花功能基因组学平台,利用组学数据挖掘了与水分胁迫相关的miRNA、 siRNA及其相关生物学功能,为棉花抗逆相关的分子功能和表观遗传机制研究、育种的改良提供了数据检索资源和理论参考。
[Abstract]:Cotton is one of the important fiber and oil crops, including more than 50 different kinds of cotton. The cotton is one of the main cultivation, by Raymond cotton (D genome) and Asiatic Cotton (A genome) two evolved natural hybrid diploid cotton. Caused by high salt and drought environment the factors of water stress, is one of the main factors restricting the cotton production. The functional genome of cotton and cotton Raymond's Asian Studies, will contribute to the production of cotton and resistance improved. Through bioinformatics method constructs Raymond S cotton function genomics platform for Asian cotton root tissue response miRNA salt stress and its target genes were identified by RNA sequencing and Degradome sequencing methods, based on the target gene function enrichment analysis and analysis of miRNA double color regulation network, I of miRNA involved in salt stress response function in For the study. At the same time, I also for Asian cotton water stress response of siRNA locus was preliminarily studied. Raymond cotton is the first complete genome sequencing of cotton seed. I compared two different versions (JGI and BGI) differences in genome sequences, and selected from JGI to version of a gene set of data. Signal transduction, transcriptional regulation, secondary metabolism, molecular transport and other ways as the core, classify the related gene family. The use of biological knowledge in related species, I constructed a protein-protein interaction network, and carries on the modular analysis and functional annotation, 91 were found with stress response, signal transduction transcriptional regulation, network module, secondary metabolism related. I'm on the existing miRNA were integrated, and prediction of downstream target genes. The basic function of genes were annotated, including GO, KEGG, MapMan, conserved structure domain and promoter of In the cis elements. Based on these results, I constructed a functional genomics platform (GraP:http://structuralbiology.cau.edu.cn/GraP/ and offers a variety of search tools. At the same time, I also provide users with a cis acting element and gene function enrichment analysis tools, to meet user demand analysis. Asian cotton has good genetic stability and stress tolerance is the root of the plant. The absorption of nutrients, hormones, and other important organs feel stress, which miRNA might be involved in stress response, root development regulation. I use small RNA sequencing and degradation technology, under the condition of salt stress on Asian cotton root tissue miRNA and its target genes were studied. Through the niRNA-seq analysis found 84 differentially expressed in response to salt stress of miRNA, part of miRNA qRT-PC R were verified. At the same time, using the method of degradation of the target gene of miRNA group For verified. GO enrichment analysis of target gene, I found miRNA changes under stress conditions may accelerate from vegetative growth to reproductive growth of cotton, the cotton early to promote their escape stress. In addition, I constructed a two-color miRNA regulatory network, and the network module functional mining, found that miRNA may indirectly involved in hormone related secondary metabolism, hormone signal transduction and regulation of biological stress (non) interaction. In addition, siRNA mediated DNA methylation in epigenetic level is involved in the regulation of stress response. I use the previous data generated for Asian cotton in response to the siRNA site of water stress were identified, according to the siRNA locus, position relation of DNA repeat elements and gene screening, and stress response of siRNA related differentially expressed genes. I GO analysis of these genes was up-regulated. The main siRNA related genes involved in stress response, signal transduction and transcriptional regulation during the transfer process, while down regulated genes mainly involved in biological molecules. This study constructed cotton functional genomics platform, using proteomics data mining and water stress related miRNA, siRNA and its biological function, molecular function for cotton resistance and the study of epigenetic mechanisms, breeding improvement provides data resources and theoretical reference.

【学位授予单位】：中国农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q943.2;S562
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本文编号：1753630