植物NBS-LRR类抗病基因及小分子RNA的比较基因组学研究

发布时间：2018-08-18 14:54

【摘要】：农作物病害是影响食品安全的世界性问题。通过利用抗病品种可以有效、经济和环境友好地解决这个问题。合理利用抗病资源需要全面理解植物抗病相关基因和调控元件的进化。本研究详细论述了植物抗病基因和相关调控小RNA的进化。首先,本研究鉴定了禾本科四个物种的抗病基因。所有的抗病基因通过比较基因组的方法定位到水稻基因组中。抗病基因发生频繁地丢失和易位,在不同物种间表现出有无的多样性。抗病基因侧翼序列的线性较低。我们将研究延伸到70个基因组,并将抗病基因聚类为抗病基因家族。从总体的水平来看抗病基因的组成,禾本科编码的抗病家族数比其他植物更多。禾本科和十字花科的抗病基因在基因组中有较多的异质基因对。在其他基因组中高度复制的N基因和Form-2基因家族在这两个科中的拷贝数都很低或者缺失,与这两个基因组较高的异质性一致。其次,本研究分析了抗病基因和靶标抗病基因的miRNA的关系。高度复制的抗病基因有较高的概率产生miRNA。普遍被miR482/2118靶标的基因在在禾本科和十字花科中没有发生有效复制。靶标抗病基因的miRNA序列与密码子对应的第一位和第二位很保守,第三位具有多样性,暗示选择来自蛋白水平,miRNA的多样化可以调控多个抗病基因。我们总结了miRNA和抗病基因的共进化模型:抗病基因发生复制,从而产生miRNA来调控高度复制的抗病基因,进而控制抗病基因的代价。最后,本研究系统分析了拟南芥和水稻小RNA位点以及周围序列的GC含量。小RNA位点的边缘有剧烈的GC波动,而小RNA位点内部的GC波动较低。另外,微小转座子的GC含量与产生小RNA的丰度是一致的。PhasiRNA位点的相位分值与GC波动相关。总之,小RNA的高GC含量和GC波动与小RNA的表达相关,这些结果可以用来提高RNAi或VIGS的沉默的效率。
[Abstract]:Crop disease is a worldwide problem affecting food safety. This problem can be effectively, economically and environmentally friendly by using disease-resistant varieties. The rational utilization of disease-resistant resources requires a comprehensive understanding of the evolution of plant disease-related genes and regulatory elements. In this study, the evolution of plant disease resistance genes and related regulatory small RNA was discussed in detail. First, resistance genes of four species of Gramineae were identified. All resistance genes were mapped to the rice genome by comparative genomes. Resistance genes are frequently lost and translocated, showing diversity among different species. The linearity of flanking sequence of disease resistance gene was lower. We extend the study to 70 genomes and cluster resistance genes into resistance gene families. At the overall level, there are more resistant families in Gramineae than in other plants. Resistance genes of Gramineae and Cruciferae have more heterologous gene pairs in genome. The highly duplicated N gene and Form-2 gene family in other genomes have very low or absent copy numbers in these two families, which is consistent with the high heterogeneity of these two genomes. Secondly, the relationship between disease resistance gene and target resistance gene miRNA was analyzed. Highly replicated resistant genes have a higher probability of producing miRNA. Genes commonly targeted by miR482/2118 do not replicate effectively in Gramineae and cruciferous families. The miRNA sequence of target resistance gene is conserved with the first and second position of codon, and the third position has diversity, suggesting that the selection of diversity from protein level can regulate multiple resistance genes. We summarize the co-evolutionary model of miRNA and disease resistance genes: the replication of disease resistance genes to produce miRNA to regulate highly replicated resistance genes and then control the cost of disease resistance genes. Finally, GC content of small RNA loci and peripheral sequences of Arabidopsis thaliana and rice were systematically analyzed. The edge of the small RNA locus fluctuated sharply, while the GC fluctuation within the small RNA locus was lower. In addition, the GC content of the microtransposon is consistent with the abundance of producing small RNA. The phase fraction of the. PhasiRNA site is correlated with the GC fluctuation. In conclusion, the high GC content and GC fluctuation of small RNA are associated with the expression of small RNA. These results can be used to improve the silencing efficiency of RNAi or VIGS.
【学位授予单位】：华中农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S432.21

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