禾本科植物MADS-box基因家族鉴定及系统进化分析

	禾本科植物MADS-box基因家族鉴定及系统进化分析
	李思巧
导师	郭振华
关键词	禾本科 Poaceae MADS-box基因家族 MADS-box gene family 系统进化 Phylogeny
摘要	开花是被子植物生命周期中至关重要的环节，直接关系到植物的繁衍和遗传因子的传递。研究植物开花的分子机理对作物的改良育种和农业生产具有重要的指导意义。MADS-box转录因子是在开花植物中广泛分布的一类重要的基因家族，其在植物生命周期的多个环节都起到关键的调控作用，从种子的发育到植株的开花结果，甚至在根系和叶片的发育中都扮演着重要的角色。在禾本科（Poaceae）中，有很多物种的MADS-box基因并未得到鉴定和研究，其中包括很多基因组已测序组装成功的物种。本研究选取涵盖禾本科两大分支六个亚科的39个代表性物种，通过生物信息学方法对其MADS-box转录因子进行鉴定和分类，并对其中功能最重要的MIKCc类型基因进行基因结构分析与共线性和正选择分析，以期发现该类型基因在结构上的异同及其进化规律。并通过在不同染色体倍性的禾本科物种中进行转录组分析，以总结不同类型MADS-box转录因子的表达模式以及不同倍性的物种的MADS-box转录因子的表达模式差异。通过研究，本文主要得到以下结论：（1）MADS-box基因家族成员的鉴定本研究在39个禾本科物种中共鉴定出MADS-box基因3146个，通过分析其数量分布情况发现在禾本科物种中，MADS-box基因的数量分布遵循如下规律：基因的拷贝数与染色体倍性成正比。与拟南芥等十字花科物种相比，禾本科物种Type Ⅰ类型基因数量显著低，Type Ⅱ类型基因数量差异不显著。通过对MIKCc类型的基因进行结构域分析总结出如下规律：各亚类群的MIKCc类型基因中，MADS结构域最为保守，K结构域在亚类型基因间存在差异，I结构域和C结构域在各亚类型内部存在差异，因此蛋白质结构域可辅助判断基因的所属类群。（2）MADS-box基因进化分析本研究通过对禾本科物种基因组进行共线性分析，以MIKCc类型基因为代表发现如下规律：MIKCc类型基因的拷贝数变化由染色体倍性引起，而非基因的串联重复。这与前期数量鉴定中发现的规律相互支撑，也与前人研究结果一致。在正选择分析中发现所有禾本科MIKCc类型的基因都受到纯化选择，通过对不同亚类群基因正选择分析结果进行比对发现其受到的选择压力遵循如下规律：功能冗余的基因受到的选择压力松弛。各亚科MIKCc类型基因Ka/Ks值也有差异：在BOP分支中，稻亚科（Oryzoideae） < 竹亚科（Bambusoideae） < 早熟禾亚科（Pooideae）；在PACMAD分支中，虎尾草亚科（Chloridoideae） < 黍亚科（Panicoideae）。（3）MADS-box基因表达量分析通过比较不同亚科的禾本科物种MADS-box基因的表达情况发现不同类型的基因的表达模式具有差异：Mα类型的基因在禾本科物种中主要在花序中高表达，Mβ类型的基因主要在花序和根中高表达，Mγ类型的基因在各个组织中都有少数基因高表达，MIKC*类型和MIKCc类型的基因主要在花序中高表达。通过对比不同倍性的植物表达情况发现，在多倍体物种中存在基因数量增加，表达量减少的现象。本研究通过上述分析，丰富了MADS-box基因在禾本科植物中的分布数据，揭示禾本科植物MIKCc类型基因结构及拷贝数变化规律，同时阐明MADS-box基因在禾本科植物内的表达模式，为后续开展MADS-box基因的研究提供理论基础和参考数据。; Flowering is one of the most significant activities in the life cycle of angiosperms, which is directly related to the reproduction of plants and the transmission of gene factors. Studying the molecular mechanism of plant flowering has important guiding significance for the improvement of crop breeding and agricultural production. MADS-box transcription factors are an important gene family widely distributed in flowering plants. They play key regulatory roles in many aspects of the plant life cycle, from seed development to plant flowering and fruiting, and they even play an important role in the root and leaf development. In the Poaceae, MADS-box genes have not been identified and studied in many species, including those whose genomes have been sequenced and assembled successfully. In this study, 39 representative species covering six subfamilies of the two major clades of Poaceae were selected, and their MADS-box transcription factors were identified and classified by bioinformatics methods. And the gene structure of the most important subfamily MIKCc was analyzed as well as the collinearity and selective pressure analysis, in order to reveal the similarities and differences in the structure and the evolutionary mechanism of this subfamily. Transcriptome analysis was performed in Poaceae species with different chromosomal ploidy to find out the expression patterns of different subfamilies of MADS-box transcription factors and the differences in expression patterns of MADS-box transcription factors in species with different ploidy. Through the research, this study mainly draws the following conclusions: (1) Identification of MADS-box gene family In this study, a total of 3144 MADS-box genes were identified in 39 Poaceae species. By analyzing their quantitative distribution, it was found that the quantitative distribution of MADS-box genes in Poaceae species followed the following rules: the number of genes increases along with the chromosomal doubling, and is affected by the quality of the genome sequencing of the species. Compared with Arabidopsis and other cruciferous species, the number of Type I genes in Poaceae species was significantly low, and the difference in the number of Type II genes was not significant. Through the domain analysis of MIKCc type genes, the following rules were concluded: among the MIKCc type genes of each subgroup, the MADS domain is the most conserved, while the K domain is different from each subgroup; the I domain and the C domain are different between each cluster in each subgroup, which indicates that the protein domain structure can assist in determining the group a gene belongs to. (2) MADS-box gene evolutionary analysis The following rules were found by collinear analysis of the genomes of Poaceae species: the number of MIKCc type genes changed along with the chromosome ploidy, rather than the tandem duplication of genes. This is mutually supported by the regularity found in quantitative identification. In th
语种	中文
	2022-05
学位授予单位	中国科学院大学
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75148
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	李思巧. 禾本科植物MADS-box基因家族鉴定及系统进化分析[D]. 中国科学院大学,2022.

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