本文選題：水平基因轉(zhuǎn)移 + 轉(zhuǎn)座子�。� 參考：《西北農(nóng)林科技大學(xué)》2017年博士論文

【摘要】：具有特定生物學(xué)功能的新基因?qū)λ猩锒际且环N重要的進(jìn)化優(yōu)勢(shì)。新基因除了可以在基因組中已有遺傳物質(zhì)的基礎(chǔ)上通過(guò)緩慢演化而產(chǎn)生,也可以直接在不同物種之間發(fā)生橫向流動(dòng),即水平基因轉(zhuǎn)移。水平基因轉(zhuǎn)移在原核生物快速進(jìn)化中發(fā)揮的重要作用已經(jīng)得到廣泛認(rèn)可。但對(duì)于多細(xì)胞真核生物而言,它們巨大且復(fù)雜的基因組使得分析流程變得極為繁瑣且低效,導(dǎo)致相關(guān)的研究非常滯后。水生動(dòng)物的生活環(huán)境及一些生物學(xué)特性可能有利于它們之間發(fā)生水平基因轉(zhuǎn)移,因此系統(tǒng)的對(duì)水生動(dòng)物中的水平基因轉(zhuǎn)移情況進(jìn)行研究有利于闡明真核生物中水平基因轉(zhuǎn)移的具體機(jī)制及普遍規(guī)律,也會(huì)加深人們對(duì)遺傳資源本質(zhì)的理解。由于真核生物中普遍存在大量的轉(zhuǎn)座子,而這些轉(zhuǎn)座子具有一定的自主性,它們的水平轉(zhuǎn)移機(jī)制可能與單拷貝基因有所不同,所以對(duì)這兩類遺傳物質(zhì)的水平轉(zhuǎn)移分別進(jìn)行了研究。一轉(zhuǎn)座子的水平轉(zhuǎn)移以凡納濱對(duì)蝦為核心物種,以一個(gè)高通量測(cè)序的拼接結(jié)果為核心數(shù)據(jù)集,通過(guò)基于多重本地/在線blast的相似性搜索、進(jìn)化分析及表達(dá)分析研究了它的轉(zhuǎn)錄組中的轉(zhuǎn)座子轉(zhuǎn)錄本,這些轉(zhuǎn)錄本參與水平轉(zhuǎn)移的情況及它們可能的生物學(xué)功能,結(jié)果如下:1.從56608條凡納濱對(duì)蝦轉(zhuǎn)錄本中鑒定出了395條高度可信的轉(zhuǎn)座子轉(zhuǎn)錄本,它們中的絕大多數(shù)都是逆轉(zhuǎn)錄轉(zhuǎn)座子的轉(zhuǎn)錄本。157條轉(zhuǎn)座子的轉(zhuǎn)錄本表現(xiàn)出與遠(yuǎn)緣物種更高的相似度,這些遠(yuǎn)緣物種主要是輻鰭魚類、貝類和寄生生物;這157條轉(zhuǎn)錄本中有83條可以確定來(lái)自于已知的凡納濱對(duì)蝦轉(zhuǎn)座子家族,對(duì)應(yīng)的轉(zhuǎn)座子家族一共是16個(gè)。2.上述的16個(gè)對(duì)蝦轉(zhuǎn)座子家族有10個(gè)已經(jīng)被注釋了編碼區(qū),因此用它們的蛋白序列與對(duì)應(yīng)的高相似同源序列進(jìn)行了進(jìn)化分析。結(jié)果表明它們?cè)谶M(jìn)化樹上的近鄰多數(shù)情況下都是水生動(dòng)物序列,而且其他水生動(dòng)物的序列之間也容易聚在一起,盡管它們之間的親緣關(guān)系非常遠(yuǎn)。3.通過(guò)與凡納濱對(duì)蝦早期發(fā)育階段和WSSV病毒重組VP28蛋白刺激下的轉(zhuǎn)錄組測(cè)序原始數(shù)據(jù)進(jìn)行短片斷比對(duì),發(fā)現(xiàn)涉及水平轉(zhuǎn)移的轉(zhuǎn)錄本有可能在抗病毒免疫中發(fā)揮了重要作用,確切的說(shuō),它們可能是抗病毒免疫的抑制因子。二單拷貝基因的水平轉(zhuǎn)移為了處理更大規(guī)模的數(shù)據(jù),首先開(kāi)發(fā)了一種基于TF-IDF(詞頻-逆文本頻率指數(shù))的水平轉(zhuǎn)移基因判斷方法。以27個(gè)分類跨度很大的物種的Uni Gene序列為核心數(shù)據(jù)集,用新開(kāi)發(fā)的方法對(duì)這些物種中的水平轉(zhuǎn)移序列進(jìn)行了初步篩選,并對(duì)這些候選序列用傳統(tǒng)的基于相似性搜索及進(jìn)化分析的方法進(jìn)行了嚴(yán)格驗(yàn)證,結(jié)果如下:1.首先從21個(gè)物種的4048個(gè)同源基因group中,使用合適的閾值,得到了20257個(gè)高度保守的基因片斷,長(zhǎng)度范圍是3-40 nt,其中數(shù)量最多的8 nt和11 nt的片斷,這些保守片斷被類比為文本中的“詞”。這些詞的分布曲線部分符合齊夫定律,而那些不符合的部分,由于TF或IDF過(guò)低,其綜合權(quán)重都很低。為了查找這些長(zhǎng)度不同的詞在序列中的出現(xiàn)次數(shù),開(kāi)發(fā)了一種動(dòng)態(tài)規(guī)劃查找算法,并用Python及C語(yǔ)言加以實(shí)現(xiàn)。2.構(gòu)造了一個(gè)基于TF-IDF的度量Dis,用來(lái)表征一條序列的特征值與該物種中所有序列平均特征值的距離。通過(guò)對(duì)序列參考不同物種得出的Dis進(jìn)行比較,可以直接判斷出哪些序列與自身物種的序列平均特征值差距大,而與其他物種的序列平均特征值差距小。采用這種方法,從13個(gè)物種判斷出了585條潛在的水平轉(zhuǎn)移序列,這些序列集中出現(xiàn)在淡水渦蟲、日本血吸蟲、貓頭鷹帽貝和肩突硬蜱中。潛在的基因供體物種也比較集中,主要是大西洋鮭、斑馬魚和安樂(lè)蜥。3.通過(guò)相似性搜索等進(jìn)一步的嚴(yán)格驗(yàn)證,從上述的585條序列中得到了63條更加可信的水平轉(zhuǎn)移序列,其中39條來(lái)自淡水渦蟲。這63條序列在眾多物種中存在高度相似的同源序列,尤其是后口動(dòng)物,但進(jìn)化分析卻表明,它們的近鄰?fù)ǔ６际沁h(yuǎn)緣的水生動(dòng)物,與用Dis預(yù)測(cè)的結(jié)果高度一致。這63條序列代表了一系列的基因,包括編碼核糖體蛋白,細(xì)胞骨架蛋白及能量代謝相關(guān)蛋白的眾多基因,它們多數(shù)都是組成性表達(dá)的管家基因。本研究的結(jié)果表明:無(wú)論是轉(zhuǎn)座子還是單拷貝基因,在水生動(dòng)物之間,特別是生態(tài)位相近的水生動(dòng)物之間都易于發(fā)生水平轉(zhuǎn)移。由于水生動(dòng)物普遍通過(guò)體外受精繁育后代,這可能就使得環(huán)境中的DNA容易在生殖細(xì)胞或胚胎階段進(jìn)入它們的細(xì)胞并整合進(jìn)基因組,進(jìn)而造成相比陸生生物更高的水平基因轉(zhuǎn)移頻率。檢測(cè)出的水平轉(zhuǎn)移單拷貝基因多數(shù)都在真核生物中普遍存在,這些基因的轉(zhuǎn)移只是對(duì)已有基因進(jìn)行了替換,卻不會(huì)引入新功能;而轉(zhuǎn)座子除非進(jìn)化成為新基因,否則它們的功能通常都是只利己的。因此總體而言,真核生物之間的水平轉(zhuǎn)移在功能上可能是以中性為主。
[Abstract]:New genes with specific biological functions are an important evolutionary advantage for all organisms. In addition to slow evolution on the basis of genetic material in the genome, new genes can also occur directly between different species, namely horizontal base shift, and horizontal gene transfer to prokaryotes. The important role played in evolution has been widely recognized. But for multicellular eukaryotes, their huge and complex genome makes the analysis process extremely tedious and inefficient, leading to the lag of related research. The living environment and some biological characteristics of aquatic animals may be beneficial to the occurrence of a horizontal base between them. As a result of the transfer, the systematic study of horizontal gene transfer in aquatic animals is beneficial to elucidate the specific mechanisms and general rules of the horizontal gene transfer in eukaryotes, and also deepen people's understanding of the nature of genetic resources. Principal, their horizontal transfer mechanism may be different from single copy genes, so the horizontal transfer of these two types of genetic material is studied respectively. The horizontal transfer of the one transposon is the core species of the Penaeus vannamei, and the result of a high throughput sequencing is the core data set, through the multiple local / online blast phase. Similarity search, evolutionary analysis and expression analysis have studied the transposon transcript in its transcriptome, the transcriptional transcripts involved in horizontal metastasis and their possible biological functions. The results are as follows: 1. the 395 highly trustworthy transposon transcripts were identified from the 56608 van shrimps transcript, the vast majority of them The transcriptional transcriptional version of the transcriptional.157 transposon of the retrotransposon shows a higher similarity with the distant species. These distant species are mainly radifishes, shellfish and parasites; 83 of these 157 transcripts can be determined from the known transposon family of Penaeus vannamei, and the corresponding transposons are 16.2. 10 of the 16 prawn transposon families have been annotated and analyzed with their protein sequences and corresponding high similarity homologous sequences. The results show that they are aquatic animal sequences in most of the adjacent adjacent trees in the evolutionary tree, and the sequences of other aquatic animals are also easily gathered together. Although the relationship between them is very far from.3. through a short short comparison with the original data of the transcriptional sequence of the WSSV virus recombinant VP28 protein stimulated by the early stage of the Penaeus vannamei and the recombinant WSSV virus, it is found that the transcriptional transcripts involved in horizontal transfer may play an important role in antiviral immunity, to be exact, they may be resistant to disease. In order to deal with more large-scale data, a horizontal transfer gene based on TF-IDF (word frequency and inverse text frequency index) was developed for the level transfer of two single copy genes. The Uni Gene sequence of 27 species with large spans was used as the core data set, and the newly developed method was used for these species. The horizontal transfer sequence was preliminarily screened, and these candidate sequences were strictly verified by traditional similarity based search and evolutionary analysis. The results are as follows: 1. first of all, 20257 highly conserved gene fragments were obtained from 4048 homologous genes of 21 species, group, and the length range was 3-40. NT, the largest number of 8 nt and 11 NT fragments, is analogous to the word "word" in text. The distribution curves of these words are in line with chill's law, and those inconforming parts, whose comprehensive weights are low due to low TF or IDF, have been developed to find the number of words of these different words in the sequence. A dynamic programming search algorithm is developed, and a TF-IDF based metric Dis is constructed with Python and C language to represent the distance between the eigenvalues of a sequence and the average eigenvalues of all the sequences in the species. By comparing the sequences of different species to the Dis in the sequence, the sequences can be directly judged by the sequences and their own species. The gap between the average eigenvalues of the sequence is large and the difference between the average characteristic values of other species is small. By this method, 585 potential horizontal transfer sequences are judged from 13 species. These sequences are concentrated in freshwater insects, Schistosoma japonicum, owl hat and Ixodes. The potential gene donor species are also concentrated, The main reason is that the Atlantic salmon, zebrafish and.3. lizard, through further rigorous verification, have obtained 63 more credible horizontal transfer sequences from the above 585 sequences, of which 39 are from freshwater vortex. These 63 sequences have highly phase similar homologous sequences among many species, especially in the posterior animal, but evolution These 63 sequences represent a series of genes, including many genes encoding ribosome proteins, cytoskeleton proteins and energy metabolism related proteins, most of which are the housekeeping genes of the constituent expression. The results showed that both the transposon and the single copy genes were easy to transfer between aquatic animals, especially the aquatic animals with similar niche. Because of the widespread use of in vitro fertilization for the aquatic animals to reproduce, it may make the DNA in the environment easy to enter their cells and integrate in the stages of the biological or embryonic stages. The gene transfer frequency is higher than that of terrestrial organisms. Most of the detected horizontal transfer single copy genes are common in eukaryotes. These genes transfer only to the existing genes, but do not introduce new functions; and the transposons do work unless they evolve into new genes. It is usually only selfish. Generally speaking, between eukaryotes horizontal transfer in function may be in neutral.
【學(xué)位授予單位】：西北農(nóng)林科技大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2017
【分類號(hào)】：Q953

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