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研究生:詹皇奕
研究生(外文):Huang-I Chan
論文名稱:發酵黴漿菌基因體定序計劃
論文名稱(外文):The genome sequence of Mycoplasma fermentans M64
指導教授:吳韋訥
指導教授(外文):Wailap Victor Ng
學位類別:碩士
校院名稱:國立陽明大學
系所名稱:生物醫學資訊研究所
學門:工程學門
學類:生醫工程學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:79
中文關鍵詞:黴漿菌基因體散彈槍定序
外文關鍵詞:Mycoplasma fermentansgenomeMycoplasmagenome sequenceshotgun
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在我們這一個發酵黴漿菌M64的基因體計劃裡,我們使用Hide and Seek的方法定序了完整的基因體,並對此基因體進行分析,它是一個圈形的染色體,長度為1118751 bp,其中平圴的鳥糞嘧啶+胞嘧啶量比例低,僅有26.9%(low GC content),而在它小而緊密的基因體中,卻有擁有相當高比例的重複序列存在其中,其中包括已知的重複序列和未知的重複序列,已知的重複序列是由4個複本的ICEF和2 個複本的噬菌體MFV1所構成,插入序列(IS element)分析的結果,我們在發酵黴漿菌中找到已知的2個家族共3種已知插入序列,ISMil、 IS1550、IS1630,另外也用dotplot分析找到可能是新的重複DNA片段,目前正在進行分析中。
我們在發酵黴漿菌基因體中找到1035個假定的基因,其中35個基因是 tRNA的基因,5個rRNA基因,接著在資料庫中經由blastp比對,找出719個蛋白質並條列出這些蛋白質功能以及相近的物種,進而將它重新整理成為Genebank的檔案格式,畫出這些基因的基因圖譜,而在這719個蛋白質中,有411個蛋白質和Mycoplasma agalactiae PG2最為相近,顯示他們在親源上的相關性,而其他沒有在資料庫被比對到假定的蛋白質,很可能就是發酵黴漿菌的特有蛋白,造成它和其他黴漿菌的不同。
COG資料庫提供了的同源基因的比對和功能性的分類,在COG的功能性分類裡,發酵黴漿菌的推定蛋白先依功能被分類為四大部份,其中和訊息儲存處理有關係的蛋白約佔38%,和代謝有關係的蛋白約佔31%,細胞訊號處理和傳導的基因有13%,而分類上不清楚的基因約佔18%。接下來從四大類的分類更進一步區分成25種功能性分類,發現在25種功能性分類中,佔最大部份比例的是分類在[J]轉譯、核糖體結構和生成以及[L]複製、重組和修復,分別佔18%和15%。
最後,我們也將定序出來的發酵微漿菌M64基因體做了二項比較,一項是和尚未完成的發酵黴菌PG18做比較,另一項則是和不經Hide and Seek方法所得到contig片段做比較,前者用來瞭解二者在定序結果上有何不同,後者則是用來說明運用Hide and Seek的策略為這個定序計劃提供的幫助。
The Mycoplasma fermentans genome has been assembled and analyzed in this study. Using the “Hide and Seek” strategy, we have assembled the whole genome shotgun sequences into a circular chromosome of 1,118,751 bp. The genome has a high percentage of repetitive sequences including 4 copies of ICEFs (Integrative conjugal element of M. fermentans), 2 copies of ΦMFV1 prophage genome, and 2 families of known IS elements (IS1550 and IS1630) identified in previous studies and several potential new transposable elements which are still being analyzed. A total of 1035 protein encoding, 35 tRNA, and 5 rRNA genes were predicted in the genome. Among the protein coding genes, 719 matched to protein sequences in the public database. Interestingly, 411 of the putative proteins are most similar to those from M. agalactiae PG2 which suggests it has close phylogenetic relationship with M. fermentans. The predicted genes were categorized after searching against the COG database. Among the 4 major COG categories, 38% of the matches belong to the “information storage and processing”, 31% metabolism, 13% cellular processes and signaling, and 18% of unclear category. When the proteins were classified according to the 25 different kinds of COG categories, the 2 biggest groups are “Translation, ribosomal structure and biogenesis“ [J] and “Replication, recombination and repair” [L] with approximately 18% and 15%, respectively. Besides, we have compared the M. fementans M64 genome with the nearly finished M. fementans PG18 in GenBank. Apparently, the “Hide and Seek” strategy is more robust in assembly, on indicated by correctly assembling the 4 copies of ICEFs in the genome.
英文摘要………………………………………………………… v
中文摘要………………………………………………………… vii
目錄……………………………………………………………… ii
圖目錄…………………………………………………………… iii
表目錄…………………………………………………………… iv
緒論……………………………………………………………… 9
材料與方法……………………………………………………… 16
結果與討論……………………………………………………… 21
參考文獻………………………………………………………… 28
附錄……………………………………………………………… 48
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