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| 植物SBP-box基因家族的系统发育、扩张模式及其与miR156的共同进化分析 | |
| Alternative Title | Phylogeny，Expansion Analysis of SBP-box Gene Family and Its Coevolution with miR156 in Plants |
| 李靖 | |
| Thesis Advisor | 刘长宁 |
| 2020 | |
| Degree Grantor | 中国科学院大学 |
| Place of Conferral | 中国科学院西双版纳热带植物园 |
| Degree Name | 理学博士 |
| Degree Discipline | 植物学 |
| Keyword | SBP-box基因家族，被子植物，裸子植物，大戟科，miR156，共线性，共进化 |
| Abstract | SBP-box基因家族是一类植物特有的转录因子基因家族，在植物中有着非常广泛的分布。由于SBP-box基因家族被发现在植物生长发育和生殖相关过程中起到了关键的调节作用而引起了人们的广泛关注。SBP-box基因家族的起源可以追溯到水生单细胞植物绿藻，陆生植物从苔藓到开花植物都检测到了SBP的分布。伴随着植物漫长的进化过程，SBP-box基因家族有着怎样的进化轨迹？它们的进化与植物的分化是否具有协同关系？我们对植物SBP-box基因家族展开了系统分析，揭示了SBP-box基因家族的扩张过程及其生物学意义，并且对SBP-box基因家族与miR156的共同进化关系展开了分析。1）被子植物是植物界最新、最具优势的一个分类。本研究选择了22个来自单子叶和双子叶共8个科的被子植物物种，对被子植物SBP-box基因家族展开了系统发育分析、基因保守性分析、扩张过程分析、与miR156的共同进化分析以及功能初步预测。我们总共得到了522个SBP基因，所有SBP基因分成11个组，这些组包括9个被子植物保守组和2个单子叶植物和双子叶植物特异组。在9个被子植物保守组中，4个组具有陆生植物保守的特征，其余5个是被子植物特异性组。这5个被子植物特有组可能与被子植物特异性功能相关。SBP基因的扩张受到miR156的影响，受到miR156调控的SBP基因倾向于保留更多的拷贝。通过组间共线性分析，揭示了不同组的动态扩张过程，发现了两条进化路径。此外，miR156与SBP存在密切的进化关系，可能来源于SBP基因的面对面（face-to-face）串联复制。没有miR156结合位点的SBP基因通常在功能上是保守的，或者像持家基因（house-keeping）类似的功能，属于陆生植物保守组。相比之下，被子植物倾向于选择具有miR156结合位点的SBP基因来调控更复杂的生理过程。2）裸子植物构成了世界上大部分的森林，是现存植物的一个重要分类，是植物进化史上一个非常重要的过渡性分支。本研究选择了6种裸子植物进行SBP基因的鉴定。为了获得更准确的鉴定结果，我们结合使用了全基因组范围和转录组范围的两种基因预测手段。74个SBP基因被鉴定得到，根据系统发育结果分成了4个簇。保守域和蛋白结构分析显示，簇间存在显著差异，而同一簇内一致性较高。蛋白质结构分析也表明，不同簇的SBP结构域外存在保守基序，这表明不同的簇之间可能存在共同的进化祖先。通过与被子植物SBP分组的比较，我们发现裸子植物SBP的系统发育分类比被子植物简单得多，这表明了被子植物与裸子植物的SBP可能出现了功能分化。另外，裸子植物与被子植物的差异主要集中在受到microRNA调控的SBP基因中，被子植物受到microRNA调控的SBP出现多个分支，说明microRNA的调控很可能促进了被子植物SBP基因的分化，也可能导致了被子植物SBP基因功能的多样化。3）大戟科是有花植物中最大的科之一。由于其生长形态的多样性和全球广泛分布的特点，自古以来就引起了人们的兴趣。我们对四种大戟科经济植物（小桐子，蓖麻，橡胶树和木薯）的SBP基因进行了全基因组的鉴定和定性。共有77个SBP基因在四个大戟科基因组中被鉴定。所有这些SBP蛋白都属于3个长度范围并且依据系统发育结果可以分成10个组。大戟科的分组策略与被子植物的分组策略相一致，进一步表明了我们的被子植物SBP分类方案具有高度的适用性。拟南芥中不存在Group-6，而大戟科中存在Group-6。片段复制在大戟科SBP基因的扩张过程中起着重要的作用，这些复制的基因都服从纯化选择。此外，大戟科约三分之二的SBP基因存在miR156的潜在调控靶点，部分miR156调控的SBP基因表达强度高，组织表达差异明显。不同胁迫处理的表达谱显示大戟科SBP基因广泛参与了各种非生物和激素处理的反应，表现出高度的功能差异性。以上研究结果说明了SBP-box基因家族在植物进化的过程中既有保守性又有特异性的进化特点。一些SBP基因展现出了广泛的保守性，呈现出陆生植物高度相似的特点；另外一些SBP基因则展现出在不同类型植物中高度分化的特性。没有microRNA调控的SBP基因普遍展现出陆生植物保守性，而受到microRNA调控的SBP基因则在不同类型植物中展现出较高的特异性。被子植物中受到microRNA调控的SBP基因分化成多个组，它们与被子植物生长、生殖过程密切相关。另外，SBP基因的进化也与特定的地质条件和历史时期紧密相关。全基因组复制事件是SBP基因分化的直接推动力。被子植物的SBP基因在不同的全基因组复制事件后呈现出不同的扩张谱图。SBP基因的进化也会受到microRNA的选择，受到microRNA调控的基因具有更高的拷贝保留数量。此外，microRNA的形成与SBP基因密切相关。我们的研究给出了一种可能的miR156出现模型。大戟科的SBP组成与拟南芥高度相似，但是个别组是大戟科保守的，却在拟南芥中缺失。个别组在拟南芥和大戟科中的差异表达谱也提供了我们深入挖掘SBP基因功能的线索 |
| Other Abstract | SBP-box gene family is a kind of plant specific transcription factor gene family, which is widely distributed in plants.The SBP-box gene family has attracted wide attention because it is found to play a key regulatory role in plant growth, development and reproduction. The origin of the SBP-box gene family can be traced back to the aquatic single-celled plant green algae, and the distribution of SBP has been detected in terrestrial plants ranging from mosses to flowering plants. As the SBP-box gene family has a long evolutionary history and features of functional diversity, what is the evolutionary trajectory of the SBP-box gene family along with the long evolutionary process of plants? Is there a synergistic relationship between their evolution and plant differentiation? In this study, we comprehensively analyzed the SBP-box gene family in plants, and revealed the dynamic evolutionary processes of SBP-box gene family and its biological significance. 1. Angiosperms are the latest and most advantageous classification in the plant kingdom. In this study, 22 angiosperms from 8 families of monocots and eudicots were selected. Phylogenetic analysis, gene conservation analysis, expansion process analysis, coevolution analysis with miR156 and preliminary functional prediction were carried out. A total of 522 SBPgenes were obtained, they were divided into11 groups.These groups included 9 angiosperm conservative groups and 2 monocotyledons-and dicotyledone-specific groups.Of the 9 angiosperm conservation groups, 4 had the characteristics of terrestrial plant conservation, and the remaining 5 were angiosperm specific groups.These five angiosperm-specificgroups show diversity in structure and function, and theymay be related to the specific functions of angiosperms.The expansion of the SBPgene is influenced by miR156, and the SBPgenesregulated by miR156 tend to retain more copies.Through syntenyanalysis, the dynamic evolution process of different groups is revealed, and two evolutionary routes are found.In addition, miR156 has a close evolutionary relationship with SBP and may be derived from face-to-face tandem replication of the SBPgene.SBPgenes without miR156 binding sites are generally functionally conserved, or similar to house-keepinggenes, and belong to the terrestrial conserved group.In contrast, angiosperms tend to choose the SBPgene with the miR156 binding site to regulate more complex physiological processes.2. Gymnosperms, which make up most of the world's forests,are an important group of living plants and a very important transitional branch in plant evolution.In this study, six gymnosperms were selected for SBPgene identification.The identification of these SBPgenes combined genome-wide and transcriptome-widepredictions.A total of 74 SBPgenes were identified and divided into 4 clusters according to phylogenetic results.Secondly, the analysis of conserved domain and protein structure showed that there were significant differences among clusters, while the consistency within clusters was high.The protein structure analysis also showed that the clusters outside the SBP structure domain had a conservative motif, which indicated that there might be a common evolutionary ancestor between the different clusters.In addition, the grouping schemes between gymnosperms and angiosperms were significantly different, indicating the functional differences between them. The groups were regulated by miR156 showed the biggest difference, suggesting the regulation of miR156 may accelerate the SBP differentiation. 3. Euphorbiaceae is one of the largest families of flowering plants.Due to the diversity of its growth forms and the characteristics of global distribution, it has aroused people's interest since ancient times.Thegenome-wide identification and characterization of SBPgenes of four economic Euphorbiaceae plants （physic nut, castor, rubber tree and cassava）were carried out.A total of 77 SBPgenes have been identified in four Euphorbiaceaegenomes.All of these SBP proteins fall into a 3-length range and can be divided into 10 groups based onthe phylogenetic tree.The grouping scheme of Euphorbiaceae is consistent with that of angiosperms, which indicates that our angiosperms SBP classification scheme is highly applicable. There wereno homologous SBPgenes of Group-6 in A.thaliana.Segmentduplicationplays an important role in the expansion of Euphorbiaceae SBP genes.In addition, about two-thirds of the SBPgenes of Euphorbiaceae are potential targets for miR156, and some of the SBPgenes regulated by miR156 have high expression intensity and obvious differences in tissue expression.The expression profiles of different stress treatments showed that the EuphorbiaceaeSBPgene was widely involved in various abiotic and hormonal responses, showing a high degree of functional variability.The above results indicate that the SBP-box gene family is both conserved and specific in the process of plant evolution.Some SBPgenes showed extensive conservation and showed highly similar characteristics in terrestrial plants.Other SBPgenes exhibit highly differentiated characteristics in different types of plants.The SBPgene without microRNA regulation generally showed the conservation interrestrial plants, while the SBPgene regulated by microRNA showed high specificity in different types of plants.The SBPgene regulated by microRNA in angiosperms is differentiated into several groups, which are closely related to the growth and reproductive process of angiosperms.In addition, the evolution of SBPgene is closely related to specific geological conditions and historical periods.Genome-wide duplicationevents are a direct driver of SBPgene differentiation.The SBPgene in angiosperms showed different expansion spectra after different genome-wide duplicationevents.The evolution of SBPgene is also selected by microRNA, and the genes regulated by microRNA have higher copy retention.In addition, the formation of microRNA is closely related to the SBPgene.Our study provides a possible model for the emergence of miR156.The SBP composition of Euphorbiaceae is highly similar to that of A. thaliana, but some groups that are conservative of Euphorbiaceae are missing in A. thaliana.The differential expression profiles of individual groups in A. thalianaand Euphorbiaceae also provide clues for us to further explore the function of SBPgene. |
| Pages | 160 |
| Language | 中文 |
| Document Type | 学位论文 |
| Identifier | https://ir.xtbg.ac.cn/handle/353005/11702 |
| Collection | 西双版纳热带植物园毕业生学位论文 |
| Affiliation | 1.中国科学院大学; 2.中国科学院西双版纳热带植物园 |
| Recommended Citation GB/T 7714 | 李靖. 植物SBP-box基因家族的系统发育、扩张模式及其与miR156的共同进化分析[D]. 中国科学院西双版纳热带植物园. 中国科学院大学,2020. |
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| 李靖.pdf（8019KB） | 学位论文 | 开放获取 | CC BY-NC-SA | Application Full Text | ||
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