本文選題：Illumina測序　切入點：單分子實時測序　出處：《昆明理工大學(xué)》2017年碩士論文

【摘要】：近年來,三代測序技術(shù)發(fā)展迅猛,本文將三代測序技術(shù)與二代測序結(jié)合,充分利用三代測序長讀長以及二代測序高精度的優(yōu)勢,降低高重復(fù)、高雜合等區(qū)域的組裝難度,得到高質(zhì)量的香菇基因組圖譜。通過對香菇基因組組裝分析,歸納出一套完整的組裝流程,對于復(fù)雜基因組的組裝具有借鑒意義。最終,使用混合組裝流程得到的香菇組裝結(jié)果的總長為45.7Mb,contigN50為630Kb,與二代組裝結(jié)果相比,我們得到的香菇基因組無論從完整性和連續(xù)性均遠遠勝出。結(jié)合abinition、Homology、EST預(yù)測的方法,最終我們共得到12511個基因,基因模型的數(shù)目為14616個,每個基因的平均長度為1952bp。使用NR數(shù)據(jù)庫、Swiss-Prot數(shù)據(jù)庫、GO數(shù)據(jù)庫、Pfam數(shù)據(jù)對基因序列進行功能注釋,其中有11255個基因能夠被功能注釋,1256個基因沒有被功能注釋。通過對于香菇基因組重復(fù)序列分析,在香菇基因組中,有21.56%的序列為重復(fù)序列,其中。反轉(zhuǎn)錄轉(zhuǎn)座子的含量約占16.48%,其中,Gypsy家族占全部基因組的12.00%,進一步研究發(fā)現(xiàn),這些轉(zhuǎn)座子的行程時間較短。非編碼RNA在生物體內(nèi)具有重要的作用,通過使用不同軟件和數(shù)據(jù)庫,在香菇基因組中,共找到tRNA317個,rRNA30 個,其中,8s、18s、28s 均為 10 個,snoRNA14 個,snRNA35 個。通過二三代基因組比較,我們發(fā)現(xiàn)它們之間存在著很多“gap”區(qū)域,通過分析發(fā)現(xiàn),很多gap區(qū)域內(nèi)部含有大量的基因和重復(fù)序列,正是因為高含量的重復(fù)序列,導(dǎo)致二代組裝結(jié)果不完整,從而缺失了很多片段。但是,基于二三代混合組裝的方法較好地解決了重復(fù)序列的問題,使最終的組裝結(jié)果更加完整。碳水化合物是自然界中最為廣泛、數(shù)量最多的一類重要化合物,依據(jù)它的功能,可以劃分為糖苷水解酶類、糖基轉(zhuǎn)移酶類、多糖裂解酶類以及糖酯酶類,在香菇基因組中,我們共鑒定出來472個碳水化合物活性酶,其中,多個基因家族與糖類、纖維素類、半纖維素等碳水化合物的講解利用有關(guān),表明香菇在利用工業(yè)廢棄物,如蔗渣、秸稈等,具有廣闊的前景。
[Abstract]:In recent years, the third generation sequencing technology has developed rapidly. In this paper, we combine the third generation sequencing technology with the second generation sequencing technology, make full use of the advantages of the long reading length of the third generation sequencing and the high precision of the second generation sequencing, and reduce the difficulty of assembling the regions such as high repetition, high heterozygosity and so on. A high-quality genome map of Lentinus edodes was obtained. By analyzing the genome assembly of Lentinus edodes, a set of complete assembly process was concluded, which is useful for the assembly of complex genome. The total length of the Lentinus edodes assembled by using the mixed assembly process was 45.7 Mbcontig N50 = 630Kb. Compared with the second generation assembly results, our obtained Lentinus edodes genome was far superior in terms of integrity and continuity. Finally, we got 12511 genes, the number of gene models was 14616, the average length of each gene was 1952bp.Using NR database Swiss-Prot database go database / Pfam data to annotate the gene sequence. Among them, 11255 genes could be annotated by function, 1256 genes were not annotated by function. By analyzing the repeat sequence of Lentinus edodes genome, 21.56% of the sequences were repeats in the genome of Lentinus edodes. Among them, the content of retrotransposons is about 16.48, and the Gypsy family accounts for 12.00 of the whole genome. Further studies show that these transposons have a shorter travel time. Noncoding RNA plays an important role in organisms. By using different software and databases, a total of 30 tRNA317 rRNAs were found in the genome of Lentinus edodes, of which 18 srRNAs were 10 snoRNAs and 14 snRNAs were found. By comparing the genomes of the second and third generation, we found that there are many "gap" regions between them. Many gap regions contain a large number of genes and repeat sequences, which lead to incomplete second-generation assembly and many missing fragments because of the high content of repeat sequences. The method based on the second and third generation hybrid assembly method solves the problem of repeated sequences and makes the final assembly result more complete. Carbohydrates are one of the most extensive and abundant important compounds in nature, depending on their functions. It can be divided into glycoside hydrolases, glycosyltransferases, polysaccharides lyase and glycosylesterases. In the genome of Lentinus edodes, we have identified 472 carbohydrate active enzymes. The explanation and utilization of carbohydrates such as hemicellulose indicate that lentinus edodes are making use of industrial wastes such as bagasse and straw.
【學(xué)位授予單位】：昆明理工大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2017
【分類號】：S646.12

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