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研究生：	林咸嘉 Lin, Hsien-Chia
論文名稱：	蝴蝶蘭葉綠體基因體之分析 Analysis of the Chloroplast Genome in Phalaenopsis aphrodite subsp. formosana
指導教授：	吳文鑾 Wu, Wen-Luan 張清俊 Chang, Ching-Chun
學位類別：	碩士 Master
系所名稱：	生物科學與科技學院 - 生物科技研究所 Institute of Biotechnology
論文出版年：	2005
畢業學年度：	93
語文別：	中文
論文頁數：	157
中文關鍵詞：	蝴蝶蘭、葉綠體基因體
外文關鍵詞：	chloroplast genome, Phalaenopsis aphrodite subsp. formosana
相關次數：	點閱：136 下載：4
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　　台灣阿嬤蝴蝶蘭(Phalaenopsis aphrodite subsp. formosana)葉綠體基因體的完整序列已經定序完成。蝴蝶蘭葉綠體基因體為雙股螺旋的DNA所組成，大小為148,964 bp，包括一對相反重複的序列(IRs)大小約為25,732 bp，被一個大單一基因區域(LSC) 和一個小的單一基因區域(SSC)所分離，大小分別約為85,947 bp和11,543 bp。基因體中共包含76個蛋白質轉錄基因，4種不同的核糖體基因，30個不同的tRNA基因。使用225 bp作為臨界點，亦定出有24個putative ORF。整個蝴蝶蘭葉綠體基因體的結構較類似於雙子葉植物，而非單子葉植物。17個基因存在內含子，包含有六個tRNA與11個蛋白質轉錄基因，其中clpP、rps12與ycf3等三個基因則有各兩個內含子。不同於其他被子植物葉綠體基因體，通常被子植物葉綠體基因體中有一組11個完整的NADH dehydrogenase基因，但是在蝴蝶蘭葉綠體基因體中則缺少ndhA、ndhH和ndhF基因，而ndhE、ndhG和ndhI有序列斷裂，並可能喪失基因功能。蝴蝶蘭葉綠體基因體基因的遺失，造成在已知的可行光合作用的被子植物葉綠體基因體，其含有最小的SSC。葉綠體基因體中的rpl2需要經過RNA編輯來產生正確的起始密碼，ndhB、ndhC、ndhD、ndhJ及ndhK則無法藉由RNA編輯來恢復其正常功能， ycf1則可能需要經由RNA編輯來恢復正常功能。Tajima’s relative rate test則顯示蝴蝶蘭葉綠體基因體中的蛋白質轉錄基因，與五種不同的禾本科單子葉植物的葉綠體基因體(水稻、甘蔗、玉米、小麥和野稻; 所有p’s<0.001)，明顯有較慢的演化速率。

　The complete nucleotide sequence of the chloroplast genome of the Taiwan moth orchid (Phalaenopsis aphrodite subsp. formosana) was determined. The circular double stranded DNA of 148,964 bp comprises a pair of inverted repeats of 25,732 bp, which is separated by a small single copy (SSC) and a large single copy (LSC) region of 11,543 and 85,957 bp, respectively. The genome contains 76 protein coding genes, 4 ribosomal RNA genes, 30 tRNA genes and 24 putative open reading frames (ORFs). Seventeen genes are intron-containing, including 6 tRNA and 11 protein coding genes. Unlike other chloroplast genomes of angiosperms, which have a complete set of genes for the 11 subunits of NADH dehydrogenase, the chloroplast genome of Phalaenopsis completely lacks the ndhA, ndhH and ndhF genes, in addition, its ndhE, ndhG and ndhI genes are truncated and probably non-functional. This loss results in the SSC region in Phalaenopsis being the shortest among known photosynthetic angiosperms. RNA editing is occurred to restore gene function of rpl2 but not ndhB, ndhC, ndhD, ndhJ and ndhK, and is hypothesized to be necessary for ycf1. Results of Tajima’s relative rate test indicates that the protein coding genes in Phalaenopsis evolved significantly more slowly than those any of the five different grasses (rice, sugarcane, maize, wheat and wild rice; all p’s<0.001) for which the complete chloroplast genome is known.

目錄
第一章、前言...............................................1
第二章、文獻探討...........................................2
   1. 植物體中葉綠體的演化與扮演的角色....................2
   2. 定序完成的葉綠體基因體..............................3
   3. 葉綠體基因體........................................5
3.1 葉綠體基因體的大小變異..........................6
3.1.1 低等植物與高等植物葉綠體基因體大小差異.....6
3.1.2 葉綠體基因所導致的葉綠體基因體大小差異.....7
3.1.3 導致葉綠體基因體大小差異的可能機制.........7
      3.2 葉綠體基因體的結構變異..........................8
3.2.1 葉綠體基因體邊界變異.......................8
3.3 葉綠體基因體所含有的基因........................9
3.3.1 葉綠體rRNA和tRNA基因.....................9
3.3.2 葉綠體蛋白質轉錄基因......................10
3.3.2.1 葉綠體核醣體基因....................10
3.3.2.2 葉綠體光合作用基因..................11
3.3.2.3 葉綠體其他基因......................12
3.4 葉綠體基因內含子(intron).........................12
3.5 葉綠體基因體的基因變異.........................14
4. 葉綠體基因轉譯.....................................14
5. 葉綠體基因體遺傳特性...............................15
6. RNA編輯 (RNA editing)...............................16
6.1 葉綠體RNA編輯.................................16
6.2 葉綠體基因RNA編輯現象.........................17
7. 葉綠體基因體的應用.................................18
8. 蘭花生化代謝特性...................................19
9. 蝴蝶蘭特性.........................................20
10. 基因體解讀計畫策略................................21
10.1 基因體載體構築.................................21
10.2 全基因體震斷定序...............................22
11. 高等植物演化......................................23
11.1 利用葉綠體基因體進行高等植物演化分析...........23
第三章、材料與方法........................................25
1. 實驗材料...........................................25
2. 實驗方法...........................................25
2.1 蝴蝶蘭葉綠體純化................................25
2.1.1 蝴蝶蘭之來源及處理.........................25
2.1.2 製備緩衝溶液及純化管柱.....................25
2.1.3 初步純化葉綠體.............................26
2.1.4 管柱純化葉綠體.............................26
2.2 純化蝴蝶蘭葉綠體DNA...........................27
     2.3 葉綠體DNA酵素切割.............................28
2.4蝴蝶蘭葉綠體Shotgun library之建立.................28
2.4.1 葉綠體DNA的片段化........................28
2.4.2 質體的構築.................................29
2.4.2.1 大量製備pBluescript載體...............29
2.4.2.2 限制酵素水解作用.....................29
2.4.2.3 平齊端接合作用.......................30
2.4.3 利用電穿孔法將DNA轉入細菌中..............30
2.4.4 質體純化與菌種保存.........................30
2.4.4.1 製備質體.............................30
2.4.4.2 菌種保存.............................31
2.4.5 DNA核酸序列定序..........................31
2.5 基因體序列分析..................................32
2.6 蝴蝶蘭RNA的製備...............................33
2.6.1蝴蝶蘭RNA的萃取..........................33
2.6.2 蝴蝶蘭RNA是否有DNA存在之檢測..........34
2.6.3 清除RNA中的DNA污染....................34
2.7 蝴蝶蘭葉綠體基因rpl2、ndhD RNA editing分析.......35
2.7.1反轉錄聚合酶連鎖反應 (RT-PCR)..............35
2.7.2質體接合反應...............................36
2.7.3 DNA序列多重排比..........................36
2.8 北方墨點反應....................................36
2.8.1 RNA分離..................................36
2.8.1.1 RNA膠體製備.........................36
2.8.1.2 RNA樣品與RNA marker製備............37
2.8.1.3 RNA電泳.............................37
2.8.2 RNA 探針(probe)製備........................37
2.8.2.1 載體製備.............................37
2.8.2.2 In vitro transcription.....................38
2.8.3 北方墨點轉漬分析..........................38
2.8.3.1 RNA轉漬.............................38
2.8.3.2 雜合溶液的製備.......................39
2.8.3.3 RNA雜合反應.........................39
2.8.3.4 呈色反應.............................40
2.9蛋白質序列多重排比(multiple alignment)..............41
2.10 rRNA與intron序列多重排比(multiple alignment)......42
2.11 取代率分析.....................................42
2.12 蝴蝶蘭演化地位分析.............................43
第四章、結果.............................................45
1. 台灣阿嬤蝴蝶蘭(TS-97)葉綠體基因體的萃取.............45
2.台灣阿嬤蝴蝶蘭(TS-97) Shot-gun library建立與基因體之定序.................................................45
3. 台灣阿嬤蝴蝶蘭(TS-97) 基因體之定序..................46
4. 台灣阿嬤蝴蝶蘭 (TS-97)葉綠體基因體分析..............46
4.1 蝴蝶蘭葉綠體基因體結構分析......................46
4.2 蝴蝶蘭葉綠體基因體基因註解......................47
4.3 蝴蝶蘭葉綠體基因體基因分類......................48
4.4 蝴蝶蘭葉綠體基因體蛋白質轉錄基因分析............49
4.5 蝴蝶蘭葉綠體密碼子使用(codon usage)...............52
5. 蝴蝶蘭葉綠體基因體RNA編輯的分析.................52
6. 蝴蝶蘭葉綠體基因體基因內含子(intron)分析.............54
7. 蝴蝶蘭葉綠體基因體邊界(junction)分析.................55
      7.1 蝴蝶蘭葉綠體ndhA、ndhE、ndhF、ndhG、ndhH和ndhI基因分析......................................56
         7.1.1 ndhA、ndhF和ndhH基因由葉綠體轉移至細胞核證據.....................................56
          7.1.2 ndhE、ndhG和ndhI基因由葉綠體轉移至細胞核證據.....................................57
8. orf91表現分析........................................57
9. 蝴蝶蘭葉綠體基因體演化速率分析......................59
9.1蛋白質轉錄基因演化速率分析......................59
9.2 蛋白質轉錄基因synonymous (Ks) 和 nonsynonymous (Ka)
代率分析........................................59
9.3 rRNA和內含子(intron)演化速率分析................60
9.4 蝴蝶蘭演化地位分析.............................61
第五章、討論..............................................63
1. 蝴蝶蘭葉綠體ndh基因................................63
2. 葉綠體基因轉移至細胞核原因及機制....................66
3.  RNA 編輯於葉綠體基因遺失所扮演角色................68
4. 蝴蝶蘭葉綠體基因體基因變異..........................69
 5. 葉綠體基因體結構差異................................70
 6. 葉綠體基因內含子(intron)比較分析......................71
7. 葉綠體基因體邊界(junction)變異........................71
8. 蝴蝶蘭葉綠體基因體應用..............................72
第六章、文獻參考..........................................74

 
圖目錄
圖一、蝴蝶蘭完整葉綠體與破裂葉綠體之梯度管柱分離..........85
圖二、蝴蝶蘭(Phalaenopsis aphrodite subsp. formosana)葉綠體基因體酵素切割圖譜.............................................86
圖三、蝴蝶蘭葉綠體基因體震斷圖............................87
圖四、Shot-gun clones的DNA分析............................88
圖五、 蝴蝶蘭(Phalaenopsis aphrodite subsp. formosana)葉綠體基因體圖譜.....................................................89
圖六、葉綠體ndhK基因DNA序列多重排比分析................91
圖七、葉綠體ndhC基因DNA序列多重排比分析...............92
圖八、葉綠體ndhJ基因DNA序列多重排比分析................93
圖九、葉綠體ndhD基因DNA序列多重排比分析...............95
圖十、葉綠體ndhE基因DNA序列多重排比分析...............96
圖十一、葉綠體ndhG基因DNA序列多重排比分析.............97
圖十二、葉綠體ndhI基因DNA序列多重排比分析..............98
圖十三、葉綠體ndhB基因DNA序列多重排比分析.............101
圖十四、葉綠體基因RNA編輯的分析........................103
圖十五、葉綠體rpl2基因RNA編輯的分析...................105
圖十六、葉綠體ndhD基因RNA編輯的分析..................107
圖十七、葉綠體基因體邊界分析.............................118
圖十八、葉綠體ndhA基因DNA序列多重排比分析.............110
圖十九、葉綠體ndhH基因DNA序列多重排比分析............112
圖二十、葉綠體ndhF基因DNA序列多重排比分析............114
圖二十一、葉綠體基因ndhA、ndhH及ndhF由葉綠體轉移至細胞核......................................................115
圖二十二、蝴蝶蘭與六種高等植物之ndhA基因部分DNA片段序列多重排比................................................116
圖二十三、蝴蝶蘭與六種高等植物之ndhA部分蛋白質序列多重排比......................................................117
圖二十四、蝴蝶蘭與六種高等植物之ndhH部分基因片段DNA序列多重排比................................................118
圖二十五、蝴蝶蘭與六種高等植物之ndhH基因部分蛋白質序列多重排比....................................................119
圖二十六、蝴蝶蘭與六種高等植物之ndhF部分基因片段DNA序列多重排比................................................121
圖二十七、蝴蝶蘭與六種高等植物之ndhF基因部分蛋白質序列多重排比....................................................122


圖二十八、葉綠體基因ndhE、ndhG及ndhI由葉綠體轉移至細胞核......................................................123
圖二十九、蝴蝶蘭與六種高等植物之ndhG部分基因片段DNA序列多重排比................................................124
圖三十、蝴蝶蘭與六種高等植物之ndhG基因部分蛋白質序列多重排比......................................................125
圖三十一、蝴蝶蘭與六種高等植物之ndhI部分基因片段DNA序列多重排比..................................................126
圖三十二、蝴蝶蘭與六種高等植物之ndhI基因部分蛋白質序列多重排比....................................................127
圖三十三 、蝴蝶蘭orf91的DNA序列比較....................128
圖三十四、蝴蝶蘭orf91的氨基酸序列比較....................129
圖三十五、利用RT-PCR偵測orf91 RNA transcripts 的存在......131
圖三十六、利用RNA blot偵測orf91 RNA transcript的存在......133
圖三十七、蝴蝶蘭與五種禾本科植物共有之65個蛋白質轉譯基因的核苷酸之同義取代(synonymous)與非同義取代(nonsynonymous)值......................................................134
圖三十八、蝴蝶蘭與五種禾本科植物所共有之四種rRNA基因與15個introns，其核苷酸transition (Ts)與transversion (Tv)之分析.....135
圖三十九、蝴蝶蘭與16種高等綠色植物之演化關係............136
 
表目錄
表一、NCBI已發表定序完成之31種高等綠色植物物種之分類地位......................................................137
表二、蝴蝶蘭葉綠體基因體所含有的基因.....................138
表三、蝴蝶蘭葉綠體基因體中含有intron的基因及其exon與intron的長度..................................................139
表四、蝴蝶蘭與其他10個物種葉綠體基因體之蛋白質序列相似性......................................................140
表五、蝴蝶蘭葉綠體基因體基因的codon usage分析............142
表六 、20種高等微管束植物的葉綠體基因ndhD、petL、psbL和rpl2的起始密碼序列..........................................143
表七、蝴蝶蘭葉綠體基因體與5種單子葉植物、2種雙子葉植物和2種裸子植物共有之 20個基因intron的長度...................144
表八、蝴蝶蘭葉綠體基因體與5種單子葉植物、2種雙子葉植物和2種裸子植物intron序列的相似性.............................145
表九、trnH和rps19基因位於被子植物葉綠體基因體的位置.....146
表十、蝴蝶蘭(Phalaenopsis aphrodite subsp. formosana)與四種單子葉植物和三種雙子葉植物的ndhA、ndhG、ndhH、ndhI和ndhF部分基因片段DNA序列之相似性.................................147
表十一、蝴蝶蘭(Phalaenopsis aphrodite subsp. formosana)與四種單子葉植物和三種雙子葉植物的ndhA、ndhG、ndhH、ndhI和ndhF基因片段的氨基酸序列之相似性................................148
 
附圖目錄
附圖一、Ndh複合體蛋白於葉綠體中所扮演可能角色...........149





附表目錄
附表一、本研究所使用到各引子序列........................150
                                    

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