臺灣博碩士論文加值系統

細菌和真菌是分布最廣的生物，自古以來便與人類的生活及歷史的演進息息相關，其中不乏各種造成過敏和瘟疫的病原，亦包含興旺食品加工及製造業的物種。然而菌相的分布會隨著時間而不斷變化，造成我們生活中的各種不確定性，為了快速鑑定真菌物種，必須找出相對較精準的方法，擬定一套標準供大家共同執行。2005年發展的「總體基因體學」，為研究環境中微生物群落基因體學的應用，在細菌使用16s 核醣體核醣核酸當作菌種的條碼基因，科學家亦將Internal transcribed spacer (ITS) 作為區分真菌物種的標準片段。我們利用MATLAB程式語言，建立一套分析不同環境真菌族群組成的系統。從美國國家生物技術資訊中心 (NCBI) 網站下載18個真菌ITS總體基因體學之研究專案的定序檔案，比對出各自所屬物種，接著我們也統計了每個物種重複出現的次數，作變異數分析（Analysis of variance，ANOVA）分析、主成分分析 (Principal Component Analysis, PCA) 作圖及繪製熱圖譜 (Heat map)。我們開發出的這套程式之後，只需要匯入真菌樣本的定序檔案，便可利用電腦自動化區分真菌族群，並能同步檢視不同實驗組在族群分布的差異。

Bacteria and fungi are the most wide spreading organisms and they affect human’s life so far since ancient time. They included thousands of allergens, pathogen, and involved in making food science and industry more thriving. However, the composition of microbiome could differ from time and space, produces much uncertainty in our life. In 2005, the development of metagenomics which study of the microorganisms genetic material recovered directly from environmental samples. The bacterial 16s ribosomal RNA sequences that can provide species-specific signature sequences useful for identification of bacteria. And the Internal transcribed spacer (ITS) were used to recognize the fungal species. We downloaded 18 sequences datasets of fungal ITS metagenomics project from NCBI. The composition of fungal microbiome of each dataset were generated by classified the fungal species of each sequence with alignment and counted the repeat times of every species. We also performed the analysis of variance (ANOVA), principal component analysis (PCA) and heat map plot. In this thesis, we developed a matlab program which can import the sequences data and can explore the interaction between fungal microbiome and environment (condition).

摘 要...........................................................................................................................iii
Abstract.........................................................................................................................iv
一、前言：....................................................................................................................1
1-1總體基因體學..........................................................................................................1
1-1-1.總體基因體學的簡介..........................................................................................1
1-1-2.總體基因體學的生物資訊學..............................................................................1
1-1-3.物種多樣性..........................................................................................................2
1-1-4.資料整合..............................................................................................................2
1-2真菌.........................................................................................................................3
1-2-1.真菌的簡介..........................................................................................................3
1-2-2.真菌的分類..........................................................................................................4
1-3 內部轉錄空白區域(Internal transcribed spacer)..................................................5
1-3-1.內部轉錄空白區域的簡介..................................................................................5
1-3-2.內部轉錄空白區域的系統發生學應用..............................................................6
1-4工具軟體.................................................................................................................6
1-5研究動機.................................................................................................................7
二、實驗材料與方法.............................................................................................8
2-1真菌總體基因體ITS序列的取得.........................................................................8
2-2資料處理與程式設計.............................................................................................8
三、結果.......................................................................................................................11
3-1所有資料彙整......................................................................................................11
3-2 數據分析.............................................................................................................11
3-2-1各研究內之族群分析.......................................................................................12
3-2-2各分組的族群比較...........................................................................................15
3-2-3所有資料集共同比較.......................................................................................16
四、討論.......................................................................................................................17
4-1分析流程與軟體比較............................................................................................17
4-2針對研究個案的分析............................................................................................17
4-3不同研究專案的比較之分析................................................................................17
五、圖...........................................................................................................................19
六、表...........................................................................................................................32
七、參考文獻...............................................................................................................33

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