葡萄KFC基因家族成员CDPK和PPCK的起源、进化和功能分析

发布时间：2018-04-14 18:30

本文选题：葡萄 + 基因组学　；参考：《南京农业大学》2016年博士论文

【摘要】：人类有8000多年的葡萄食用历史。现今葡萄是全球栽培面积第一和产量位居第三的水果,极具重要的经济价值和历史文化价值。作为非模式植物,葡萄中的代表欧亚种黑比诺葡萄已经完成了全基因组n,序,标志着研究水平进入了后基因组时代。在后基因组时代,两方面的研究是比较热门的,包括从上至下的某个性状的分子调控机制,和从下到上的研究某一类分子的生物学功能。本学位论文研究以转录组序列测序和比较基因组分析为主,辅以qPCR实验验证,综合了生物信息学的信息挖掘技术和数理统计分析,基于多种手段的表达分析,从分子进化-发育的角度,全面分析了葡萄CDPK基因和PPCK基因的联系,具体获得了如下成果:1.首先基于对葡萄等有代表性类群的植物基因组和转录组数据分析,发现CDPK基因和PPCK基因是同一个融合基因祖先的后代,随着进化该祖先基因后代形成一个基因单系群,该单系群祖先基因至少起源于红藻祖先中,由于该基因单系群目前还没有名字,本研究根据其结构和起源特点命名为激酶合钙调素基因家族(简称KFC基因家族)。CDPK的起源可以追溯到红藻祖先,而PPCK基因只能追溯到裸子植物祖先。基于大量不同物种中KFC基因家族成员转录分析、结构特点和数目扩增变化等综合发现,KFC的进化对于植物适应环境进化中的6个大转变均具有重要作用。2.在包括葡萄的植物内,通过比较包括CDPK基因在内的KFC基因家族钙信号转换系统与另一个主要的钙信号转换系统CIPK-CBBL,从数目、亚细胞定位、参与的功能种类、工作机制的多样性,KFC系统都是包括葡萄在内的植物界中钙信号转导系统中主要的钙信号转换系统。3.以完成基因组测序的黑比诺葡萄单倍体基因组为基础,综合使用生物信息学挖掘基因组和转录组数据,以及通过分子生物学实验验证和文本挖掘技术,发现了葡萄17个CDPK基因,揭示他们都至少诞生于有一亿年以前的基因复制,随着长期的负选择过程,从持家型表达的CDPK基因产生了 4个花粉特异表达的葡萄CDPK基因,对于后续基于这些基因开发雄性不育植株和开发无籽葡萄具有较高理论价值。同时发现了一些参与响应旱、寒、盐信号转导的葡萄CDPK基因,对于研究三个非生物胁迫信号之间的互作有参考价值。4.为研究PPCK基因的功能,新测定了 3个CAM光合作用类型兰花在昼夜不同时间的共6个转录组,比较了葡萄等双子叶植物的基因组,和共计13种兰花的转录组,均具有良好的覆盖度和测序质量,利用转录组数据挖掘出82个单拷贝细胞核基因,构建了兰花物种树,将兰科植物分为5个亚科。公开了6个转录组数据对于学界后续挖掘利用提供了一定基础。5.挖掘了不同光合作用类型兰花的PPCK基因,通过与葡萄等双子叶植物进行比较,分析发现兰科植物内PPCK基因经复制产生了两个类群,其中的一个类群表现了在13个碳固定基因家族中最明显的昼夜节律表达模式,并且具有4个激酶结构域特异的位点。6.根据PPCK, ME, PPDK,和PEPC表达模式的特点和催化反应的特点,提出了 CAM光合作用中一个新的不同于PPCK-PEPC介导,而由ME-PPDK催化的代谢通路。
[Abstract]:Humans have 8000 years of history. It is edible grape grape cultivation area and production ranks first in global third fruits, economic value and historical cultural value very important. As a non model plant, on behalf of the grapes in the Eurasian Pinot Noir has completed the whole genome sequence, N, marks the level of research into the post genome the times. In the post genome era, two aspects of research are popular, including from a trait to the molecular regulation mechanism, biological function and research from the bottom to the top of a class of molecules. In this thesis, the research on transcriptome sequencing and comparative genomic analysis, supplemented by qPCR experiment validation, comprehensive bioinformatics analysis of information mining technology and statistical analysis, the expression of a variety of means based on the development of molecular evolution - from the perspective, a comprehensive analysis of the grape CDPK gene and PPCK The specific gene, and obtained results as follows: 1. based on the analysis of the representative groups of plant genome and transcriptome data of the grape, found that CDPK gene and PPCK gene with a fusion gene of ancestry, with the evolution of the ancestral gene offspring form a monophyletic group of genes, the single ancestral gene at least originated in the red ancestors, because the gene monophyletic group currently has no name, according to the study of the structure and characteristics of origin named kinase combined calmodulin gene family (KFC family).CDPK origin can be traced back to the red ancestors, while the PPCK gene can only be traced back to gymnosperm ancestors. Analysis of a large number of members different species of KFC gene transcription based on the structural characteristics and the number of amplified discovery changes, the evolution of KFC.2. plays an important role in plant adaptation to 6 major changes in the evolution of environment In grape plants, the KFC gene family of calcium signal conversion system including CDPK gene and another calcium signal conversion system mainly from CIPK-CBBL, the number of species involved in the subcellular localization, functional diversity, the working mechanism of KFC system are the calcium signal transduction system, including grape plants in the main calcium signal conversion system.3. to complete genome sequencing of the Pinot Noir grape haploid genome based, integrated bioinformatics mining genome and transcriptome data, as well as through molecular biology experiment and text mining technology, found 17 grape CDPK genes, they reveal at least was born one hundred million years ago the gene duplication, with negative selection during the long-term expression of CDPK gene from housekeeping has produced 4 pollen specific expression of CDPK gene of grape, for the follow-up basis In the development of gene of male sterile plants and development of seedless grapes have high theoretical value. At the same time that some involved in response to drought, cold, salt grape CDPK gene signal transduction, for the study of three abiotic stress signaling interaction among the reference value of.4. for the study of PPCK function based on the new 3 CAM photosynthesis a total of 6 types of orchid group in different time of the circadian transcription was determined, compared the grapes and other dicotyledonous plant genome and transcriptome, a total of 13 species of orchids, with coverage and good quality sequencing, using transcriptome data picking up 82 single copy nuclear gene, construct the orchid species tree, will orchid plants are divided into 5 subfamilies. Discloses 6 transcriptome data for the subsequent academic mining provides a certain basis for.5. mining PPCK gene in different types of photosynthesis of orchids, with two cotyledons of grape Plants were compared, analysis showed that PPCK gene of Orchidaceae by replication produced two groups, one group which showed circadian rhythm in 13 fixed carbon gene family in the most obvious expression pattern, and has 4 sites of.6. kinase domain specific to PPCK, ME, PPDK, and PEPC expression characteristics the characteristics and reaction mode, put forward a new CAM in photosynthesis is different from the PPCK-PEPC mediated by the metabolic pathway catalyzed by ME-PPDK.

【学位授予单位】：南京农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S663.1

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