本文關(guān)鍵詞：原核生物基因組寡核苷酸轉(zhuǎn)移概率偏倚的物種特異性及致病關(guān)聯(lián)性　出處：《華南理工大學(xué)》2012年碩士論文　論文類型：學(xué)位論文

  更多相關(guān)文章： 原核生物 三核苷酸轉(zhuǎn)移概率偏倚 分子進(jìn)化 物種特異性 致病性

【摘要】：寡核苷酸使用模式及偏倚是基因組組成的一個(gè)重要特征，體現(xiàn)了個(gè)體的全部遺傳信息在堿基水平上的分布，部分寡核苷酸的過(guò)量出現(xiàn)可能會(huì)導(dǎo)致一些遺傳性疾病的發(fā)生。然而，關(guān)于寡核苷酸使用模式的偏倚是否具有種群特異性并反映種群的生物學(xué)特征這一問(wèn)題，尚未闡明。鑒于此，本文基于一階馬爾可夫鏈模型，提出了一個(gè)度量寡核苷酸使用模式偏倚的新指標(biāo)—－基因組三核苷酸（trinucleotide, tri-）轉(zhuǎn)移概率偏倚（transitionprobability bias, TPB）特征向量，或稱之為三核苷酸轉(zhuǎn)移概率最大偏倚分布，并利用該指標(biāo)研究了原核生物基因組組成和分布的偏倚特征，及其與菌株的生物學(xué)特征的關(guān)聯(lián)性。主要研究?jī)?nèi)容包括以下四個(gè)方面： 一、通過(guò)分析727條有代表性的原核生物基因組序列間tri-TPB特征向量的相關(guān)性，研究了不同的原核生物基因組間三核苷酸轉(zhuǎn)移概率最大偏倚分布的相似性，以及這種相似性與序列的G+C含量之間的關(guān)系。首次發(fā)現(xiàn)：基因組tri-TPB特征向量具有物種特異，親緣關(guān)系越近的物種，它們的tri-TPB特征向量越相似；同種內(nèi)的不同菌株具有幾乎完全相同的tri-TPB特征向量，并且不依賴于基因組的G+C含量。 二、通過(guò)分析原核生物基因組與其質(zhì)粒序列、噬菌體序列以及水平轉(zhuǎn)移基因之間tri-TPB特征向量的相關(guān)性，發(fā)現(xiàn)與原核生物基因組進(jìn)化密切相關(guān)的外源性基因元素，它們與宿主基因組之間tri-TPB特征向量的相關(guān)性高于與其他非宿主基因組的相關(guān)性，，且這種相關(guān)性隨著親緣關(guān)系的逐漸疏遠(yuǎn)而逐漸減小。 三、通過(guò)對(duì)具有不同宿主的33個(gè)dsDNA和dsRNA病毒的基因組tri-TPB特征向量進(jìn)行相關(guān)性分析，發(fā)現(xiàn)病毒基因組與原核生物基因組的三核苷酸轉(zhuǎn)移概率偏倚的分布特征不同，即病毒基因組tri-TPB特征向量不具有種內(nèi)特異性，且它們的三核苷酸轉(zhuǎn)移概率最大偏倚的差異與宿主的特異性無(wú)關(guān)。 四、分析了具有不同的致病性特征以及具有不同宿主的近緣細(xì)菌基因組間tri-TPB特征向量的相關(guān)性，并將其與基于SSU rRNA基因序列的傳統(tǒng)系統(tǒng)發(fā)育分析結(jié)果進(jìn)行比較。我們發(fā)現(xiàn)，基因組tri-TPB特征向量的相似性與菌株的致病性或宿主的特異性等生物學(xué)特征相關(guān)聯(lián)，而這種關(guān)聯(lián)性通常不能從傳統(tǒng)的系統(tǒng)發(fā)育分析中獲得，并可能被傳統(tǒng)分析方法所曲解。 本研究建立了一套基于三核苷酸轉(zhuǎn)移概率最大偏倚的基因組組成和分布的分析方法，確立了原核生物基因組tri-TPB向量的物種特異性和致病特征的關(guān)聯(lián)性，為基于全基因組寡核苷酸組成和分布信息的物種及其致病性的進(jìn)化分析提供了新的思路。
[Abstract]:The usage pattern and bias of oligonucleotides is an important feature of genome composition, which reflects the distribution of all genetic information of individuals at base level. The excessive occurrence of partial oligonucleotides may lead to the occurrence of some hereditary diseases. However, the question of whether the bias of the use pattern of oligonucleotides is population specific and reflects the biological characteristics of the population. In view of this, based on the first-order Markov chain model, a new index to measure the bias of oligonucleotide usage pattern, genomic trinucleotide, is proposed. The transition probability bias (TPB) eigenvector is known as the maximum bias distribution of trinucleotide transfer probability. The bias characteristics of the genomes composition and distribution of prokaryotes and their relationship with the biological characteristics of the strain were studied by using this index. The main contents of the study included the following four aspects: One is to analyze the correlation between tri-TPB eigenvector of 727 representative prokaryotes. The similarity of maximum bias distribution of trinucleotide transfer probability among different prokaryotes was studied. And the relationship between the similarity and the G C content of the sequence. For the first time, it was found that the genome tri-TPB characteristic vector had species-specific, and the closer the genetic relationship was, the more close the species was. The more similar their tri-TPB Eigenvectors are; Different strains of the same species have almost identical tri-TPB Eigenvectors and do not depend on the G C content of the genome. Secondly, the correlation of tri-TPB characteristic vectors between the prokaryote genome and its plasmid sequence, phage sequence and horizontal transfer gene was analyzed. The exogenous gene elements closely related to the evolution of prokaryote genomes were found to have a higher correlation with the tri-TPB characteristic vectors between the host genomes than with other non-host genomes. And this correlation gradually decreased with the gradual alienation of the kinship. Thirdly, the genomic tri-TPB characteristic vectors of 33 dsDNA and dsRNA viruses with different hosts were analyzed. It was found that the distribution characteristics of trinucleotide transfer probability bias of virus genome and prokaryote genome were different, that is, the tri-TPB characteristic vector of virus genome had no intraspecific characteristics. The difference in the maximum bias of the trinucleotide transfer probability was independent of the host specificity. Fourthly, the correlation of tri-TPB characteristic vectors among the genomes of relative bacteria with different hosts and different pathogenicity was analyzed. The results of phylogenetic analysis based on SSU rRNA gene sequence were compared. The similarity of genomic tri-TPB feature vectors is associated with biological characteristics such as pathogenicity or host specificity, which is not usually derived from traditional phylogenetic analysis. And may be misinterpreted by traditional analytical methods. In this study, a set of methods for the analysis of genome composition and distribution based on the maximum bias of trinucleotide transfer probability were established. The relationship between species-specificity and pathogenicity of tri-TPB vector of prokaryote genome was established. It provides a new idea for the evolutionary analysis of species and their pathogenicity based on the information of oligonucleotide composition and distribution.
【學(xué)位授予單位】：華南理工大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2012
【分類號(hào)】：R346

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