切叶蚁等级特异的RNA编辑组和比较研究
发布时间：2018-07-20 14:32
【摘要】：真社会性生物是指一类形成了高度社会化组织的生物,其主要特点包括:存在两个或者更多世代重叠,很多成虫生活在一起并实行合作育幼,存在生殖个体和非生殖个体间的等级分化。在真社会性昆虫中,同一群体内部的不同个体间都具有相同的基因组组成,但是不同等级间的个体在形态特征、生殖分工和行为表型等方面却存在极大的差异。表观遗传机制对于真社会性生物的非遗传多型性具有重要的调节作用。RNA编辑作为一种转录后修饰机制,是指在基因的转录物上增加、删除或取代某些核苷酸,使RNA序列不同于基因组模板上的DNA序列的过程。最近的研究表明RNA编辑在转录后调节水平上,增加了基因产物的多样性,特别对于神经系统相关功能具有重要的调控作用。因此,真社会性昆虫神经系统中的RNA编辑可能是群体内部等级分化,劳动分工的潜在调节机制。为了研究RNA编辑对于真社会性昆虫等级分化、劳动分工的可能作用,以及对于相关功能基因的调控,我们选取切叶蚁作为研究物种,并且对于不同雌性等级的头部样品进行链特异性的RNA高通量测序。我们自主研发了一款灵活、高效的软件包,用于切叶蚁RNA编辑的检测和研究。此外,我们利用其它具有基因组的蚂蚁物种数据进行比较分析。本研究的主要结论和创新点列举如下:(1)相对于其它RNA编辑检测研究,我们自主研发的RNA编辑检测软件的优势在于:利用贝叶斯模型,通过对DNA高通量测序数据进行严格的统计分析预测基因组上的纯合位点,作为后选的编辑位点。此外,该软件根据二项分布统计模型和多重严格过滤来降低由于测序错误或者序列比对错误导致的假阳性。该软件不仅可以处理单个二倍体样品,还可以处理多个个体混合的多倍体样品。(2)我们第一次报道了真社会性昆虫--切叶蚁的RNA编辑图谱。切叶蚁中的RNA编辑位点绝大多数是A-I类型编辑。这些切叶蚁中的A-I类型RNA编辑位点具有和人,小鼠和果蝇相同的特征,说明腺苷脱氨酶ADAR的功能是高度保守的。(3)通过比较不同等级的RNA编辑,我们在处女蚁后,大工蚁和小工蚁中鉴定了大约11000个编辑位点,并且这些编辑位点分布于800多个基因。这些RNA编辑的基因具有神经传导,生物节律,温度感知,RNA剪接和羧酸合成相关。(4)切叶蚁中的大多数RNA编辑都是物种特异的,只有8-23%的编辑位点在不同蚂蚁亚科中是保守的。这些位点可能对于蚂蚁的真社会性进化具有重要作用。(5)在不同等级间存在差异编辑水平的编辑位点,这表明RNA编辑可能是调节蚂蚁不同等级间行为分化的普遍机制。综上,我们的结果表明蚂蚁和其他真社会性昆虫的等级分化可能受到RNA编辑机制的调控。RNA编辑可能是一个全新,并且广泛存在的机制,通过调节神经系统中基因表达来实现不同等级间的形态差异和行为分化。
[Abstract]:A true social organism is a class of organisms that form highly socialized tissues, the main characteristics of which include: two or more generations overlap, many adults live together and work together to raise young. There is hierarchical differentiation between reproductive and non-reproductive individuals. In the true social insects, different individuals within the same population have the same genome composition, but there are great differences in morphological characteristics, reproductive division of labor and behavioral phenotypes among individuals of different levels. The epigenetic mechanism plays an important role in regulating the non-genetic polymorphism of eusocial organisms. RNA editing, as a post-transcriptional modification mechanism, refers to the addition, deletion or substitution of certain nucleotides to the transcripts of genes. The process of differentiating RNA sequences from DNA sequences on genomic templates. Recent studies have shown that RNA editing increases the diversity of gene products at the post-transcriptional level, especially plays an important role in regulating nervous system related functions. Therefore, RNA editing in the nervous system of the true social insects may be a potential regulatory mechanism for the differentiation and division of labor within the population. To study the possible role of RNA editing in the differentiation, division of labor, and regulation of related functional genes in eusocial insects, we selected leaf-cutting ants as the study species. High throughput sequencing of strand specific RNA was performed on head samples of different female grades. We have developed a flexible and efficient software package for the detection and research of leaf-cutting ant RNA editing. In addition, we used data from other ant species with genomes for comparative analysis. The main conclusions and innovations of this study are listed as follows: (1) compared with other RNA editing and detection research, the advantages of our own developed RNA editing detection software are: using Bayesian model, The homozygous sites in genome were predicted by strict statistical analysis of high-throughput DNA sequencing data. In addition, the software reduces false positives caused by sequencing errors or sequence alignment errors based on binomial distribution statistical model and multiple strict filtering. The software can not only deal with single diploid sample, but also deal with multiple individuals mixed polyploid sample. (2) We first reported the RNA editing map of the true social insect, leaf-cutting ant. The vast majority of RNA editing sites in leaf-cutting ants are A-I type editing. The A-I type RNA editing sites in these leaf-cutting ants have the same characteristics as humans, mice and Drosophila, suggesting that the function of adenosine deaminase ADAR is highly conserved. (3) by comparing different levels of RNA editing, we were in the virgin queen. About 11000 editing sites were identified in large and small worker ants and distributed in more than 800 genes. These RNA-edited genes are related to neural conduction, biological rhythm, temperature sensing RNA splicing and carboxylic acid synthesis. (4) most RNA editing sites in leaf-cutting ants are species-specific, and only 8-23% of the editing sites are conserved in different ant subfamilies. These sites may play an important role in the evolution of the true sociality of ants. (5) there are different editing sites at different levels, which suggests that RNA editing may be a universal mechanism to regulate the behavioral differentiation between different levels of ants. In summary, our results suggest that the hierarchical differentiation of ants and other eusocial insects may be regulated by RNA editing mechanisms. RNA editing may be a new and widespread mechanism. By regulating gene expression in the nervous system, morphological differences and behavioral differentiation among different grades are realized.
【学位授予单位】：华南理工大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q963
，
本文编号：2133844
[Abstract]:A true social organism is a class of organisms that form highly socialized tissues, the main characteristics of which include: two or more generations overlap, many adults live together and work together to raise young. There is hierarchical differentiation between reproductive and non-reproductive individuals. In the true social insects, different individuals within the same population have the same genome composition, but there are great differences in morphological characteristics, reproductive division of labor and behavioral phenotypes among individuals of different levels. The epigenetic mechanism plays an important role in regulating the non-genetic polymorphism of eusocial organisms. RNA editing, as a post-transcriptional modification mechanism, refers to the addition, deletion or substitution of certain nucleotides to the transcripts of genes. The process of differentiating RNA sequences from DNA sequences on genomic templates. Recent studies have shown that RNA editing increases the diversity of gene products at the post-transcriptional level, especially plays an important role in regulating nervous system related functions. Therefore, RNA editing in the nervous system of the true social insects may be a potential regulatory mechanism for the differentiation and division of labor within the population. To study the possible role of RNA editing in the differentiation, division of labor, and regulation of related functional genes in eusocial insects, we selected leaf-cutting ants as the study species. High throughput sequencing of strand specific RNA was performed on head samples of different female grades. We have developed a flexible and efficient software package for the detection and research of leaf-cutting ant RNA editing. In addition, we used data from other ant species with genomes for comparative analysis. The main conclusions and innovations of this study are listed as follows: (1) compared with other RNA editing and detection research, the advantages of our own developed RNA editing detection software are: using Bayesian model, The homozygous sites in genome were predicted by strict statistical analysis of high-throughput DNA sequencing data. In addition, the software reduces false positives caused by sequencing errors or sequence alignment errors based on binomial distribution statistical model and multiple strict filtering. The software can not only deal with single diploid sample, but also deal with multiple individuals mixed polyploid sample. (2) We first reported the RNA editing map of the true social insect, leaf-cutting ant. The vast majority of RNA editing sites in leaf-cutting ants are A-I type editing. The A-I type RNA editing sites in these leaf-cutting ants have the same characteristics as humans, mice and Drosophila, suggesting that the function of adenosine deaminase ADAR is highly conserved. (3) by comparing different levels of RNA editing, we were in the virgin queen. About 11000 editing sites were identified in large and small worker ants and distributed in more than 800 genes. These RNA-edited genes are related to neural conduction, biological rhythm, temperature sensing RNA splicing and carboxylic acid synthesis. (4) most RNA editing sites in leaf-cutting ants are species-specific, and only 8-23% of the editing sites are conserved in different ant subfamilies. These sites may play an important role in the evolution of the true sociality of ants. (5) there are different editing sites at different levels, which suggests that RNA editing may be a universal mechanism to regulate the behavioral differentiation between different levels of ants. In summary, our results suggest that the hierarchical differentiation of ants and other eusocial insects may be regulated by RNA editing mechanisms. RNA editing may be a new and widespread mechanism. By regulating gene expression in the nervous system, morphological differences and behavioral differentiation among different grades are realized.
【学位授予单位】：华南理工大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q963
，
本文编号：2133844
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