切葉蟻等級特異的RNA編輯組和比較研究
發(fā)布時間：2018-07-20 14:32
【摘要】：真社會性生物是指一類形成了高度社會化組織的生物,其主要特點包括:存在兩個或者更多世代重疊,很多成蟲生活在一起并實行合作育幼,存在生殖個體和非生殖個體間的等級分化。在真社會性昆蟲中,同一群體內(nèi)部的不同個體間都具有相同的基因組組成,但是不同等級間的個體在形態(tài)特征、生殖分工和行為表型等方面卻存在極大的差異。表觀遺傳機制對于真社會性生物的非遺傳多型性具有重要的調(diào)節(jié)作用。RNA編輯作為一種轉(zhuǎn)錄后修飾機制,是指在基因的轉(zhuǎn)錄物上增加、刪除或取代某些核苷酸,使RNA序列不同于基因組模板上的DNA序列的過程。最近的研究表明RNA編輯在轉(zhuǎn)錄后調(diào)節(jié)水平上,增加了基因產(chǎn)物的多樣性,特別對于神經(jīng)系統(tǒng)相關(guān)功能具有重要的調(diào)控作用。因此,真社會性昆蟲神經(jīng)系統(tǒng)中的RNA編輯可能是群體內(nèi)部等級分化,勞動分工的潛在調(diào)節(jié)機制。為了研究RNA編輯對于真社會性昆蟲等級分化、勞動分工的可能作用,以及對于相關(guān)功能基因的調(diào)控,我們選取切葉蟻作為研究物種,并且對于不同雌性等級的頭部樣品進行鏈特異性的RNA高通量測序。我們自主研發(fā)了一款靈活、高效的軟件包,用于切葉蟻RNA編輯的檢測和研究。此外,我們利用其它具有基因組的螞蟻物種數(shù)據(jù)進行比較分析。本研究的主要結(jié)論和創(chuàng)新點列舉如下:(1)相對于其它RNA編輯檢測研究,我們自主研發(fā)的RNA編輯檢測軟件的優(yōu)勢在于:利用貝葉斯模型,通過對DNA高通量測序數(shù)據(jù)進行嚴格的統(tǒng)計分析預(yù)測基因組上的純合位點,作為后選的編輯位點。此外,該軟件根據(jù)二項分布統(tǒng)計模型和多重嚴格過濾來降低由于測序錯誤或者序列比對錯誤導(dǎo)致的假陽性。該軟件不僅可以處理單個二倍體樣品,還可以處理多個個體混合的多倍體樣品。(2)我們第一次報道了真社會性昆蟲--切葉蟻的RNA編輯圖譜。切葉蟻中的RNA編輯位點絕大多數(shù)是A-I類型編輯。這些切葉蟻中的A-I類型RNA編輯位點具有和人,小鼠和果蠅相同的特征,說明腺苷脫氨酶ADAR的功能是高度保守的。(3)通過比較不同等級的RNA編輯,我們在處女蟻后,大工蟻和小工蟻中鑒定了大約11000個編輯位點,并且這些編輯位點分布于800多個基因。這些RNA編輯的基因具有神經(jīng)傳導(dǎo),生物節(jié)律,溫度感知,RNA剪接和羧酸合成相關(guān)。(4)切葉蟻中的大多數(shù)RNA編輯都是物種特異的,只有8-23%的編輯位點在不同螞蟻亞科中是保守的。這些位點可能對于螞蟻的真社會性進化具有重要作用。(5)在不同等級間存在差異編輯水平的編輯位點,這表明RNA編輯可能是調(diào)節(jié)螞蟻不同等級間行為分化的普遍機制。綜上,我們的結(jié)果表明螞蟻和其他真社會性昆蟲的等級分化可能受到RNA編輯機制的調(diào)控。RNA編輯可能是一個全新,并且廣泛存在的機制,通過調(diào)節(jié)神經(jīng)系統(tǒng)中基因表達來實現(xiàn)不同等級間的形態(tài)差異和行為分化。
[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.
【學位授予單位】：華南理工大學
【學位級別】：博士
【學位授予年份】：2016
【分類號】：Q963
，
本文編號：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.
【學位授予單位】：華南理工大學
【學位級別】：博士
【學位授予年份】：2016
【分類號】：Q963
，
本文編號：2133844
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