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研究生：	劉育彰 Liu, Yu-Jhang
論文名稱：	台灣原生種姬蝴蝶蘭粒線體基因組的分析 Analysis of mitochondrial genome from Phalaenopsis equestris
指導教授：	張清俊 Chang, Ching-Chung
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：	2011
畢業學年度：	99
語文別：	中文
論文頁數：	144
中文關鍵詞：	姬蝴蝶蘭、粒線體基因組、重複性序列
外文關鍵詞：	Phalaenopsis equestris, mitochondrial genome, repetitive sequences
相關次數：	點閱：153 下載：7
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粒線體經由α-proteobacteria內共生演化而來的，它們有獨立的轉錄和轉譯系統。而在哺乳類粒線體基因組之基因組成緊密，其大小約16 kb，但植物粒線體的基因組規模(200~2,400 kb)和歧異度都比動物大許多。到目前為止，根據NCBI資料庫，只有25種陸生植物的粒線體基因組已被完全解序。而蝴蝶蘭花期長，花型優美，在台灣是很重要的經濟花卉植物。台灣有二個原生種，分別是台灣白花蝴蝶蘭(P. aphrodite subsp. formosana)和桃紅姬蝴蝶蘭(P. equestris)，這二個原生種常被使用在商業育種上做為親本，進一步的雜交出各種花色和新的品種。然而，蝴蝶蘭粒線體基因組卻仍無任何研究。本研究，利用來自稻米和菸草粒線體的19個基因做為探針和9個BAC尾端探針混合，篩選姬蝴蝶蘭BAC (Bacterial Artificial Chromosome) library (含41,472 BAC clones的高密度膜)，共篩選出177個可能含有粒線體DNA 之BAC clones。進一步的藉由Dot-blots和7種粒線體基因探針篩選出39 clones可能含有粒線體DNA的BAC clones，利用脈衝式電泳(PFGE)確認DNA片段平均長度介於80~100 kb，再利用限制片段多型性(RFLP)分析做為BAC clones之指紋鑑定(fingerprinting)，並將有重疊的BAC clones分成四個群組，並進一步挑選4個BAC clones做定序及基因註解。其中BAC-25(82 kb)含有6個粒線體基因和1個偽基因，並發現粒線體rps10基因不存在於其他單子葉植物的粒線體基因組中。BAC-25含有相同2個來自葉綠體6個基因組成的2.7 kb基因組片段。此外，BAC-25富含小片段重複性序列(19~20 nt)和4個大片段重複性序列(>12 kb)。因此，BAC-25極可能含有姬蝴蝶蘭粒線體基因組之部份片段。

Mitochondria are endosymbiotic from α-proteobacteria during evolution. Mammalian mitochondrial genomes are compact with approximately 16 kb in length; in contrast, plant mitochondria genomes are diverse and range from 200 to 2,400 kb in size. Up to date, according to NCBI database, only 25 species of land plants, their mitochondrial genome have been completely determined. Phalaenopsis orchid is a fascinating flower and an economically important floral crop in Taiwan. There are two native Phalaenopsis orchid species in Taiwan, P. aphrodite subsp. formosana and P. equestris, which they have been commonly used in commercial breeding program. However, the mitochondria and their genome were less studied. In this study, we have screened the high density filters which contained 41,472 Bacterial Artificial Chromosome (BAC) clones of P. equestris with 19 probes of heterologous mitochondrial DNA and 9 probes of BAC end fragments. One hundred seventy seven BAC clones which potentially contain the mitochondrial DNA were selected. Thirty nine mitochondrial DNA containing BAC clones were further identified with 7 individual probes by Dot-blots. The insert sizes of BAC clones were determined to be 80 to 100 kb in average by PFGE (pulsed field gel electrophoresis). RFLP (restriction fragment length polymorphism) analyses and cross hybridization were used to cluster 39 BAC clones into four major overlapping groups. Four selected BAC clones were further sequenced by Solexa system. BAC-25 (82 kb) which contained 6 mitochondrial genes and 1 pseudogene was identified. The rps10 is present in BAC-25, but not found in the sequenced mitochondrial genomes of monocots so far. In addition, BAC-25 had two identical 2.7 kb regions which each consist of 6 chloroplast genes of P. equestris. Furthermore, BAC-25 contained very abundant of small repetitive sequences (19~20 nt) and 2 pairs of large directed repeats (>12 kb). Therefore, it is very likely that BAC-25 is part of mitochondrial genome of P. equestris.

目錄
第一章、前言 .............................................. 1
第二章、文獻探討 ........................................... 2
1.植物粒線體之演化和功能 .................................. 2
2.粒線體基因組 ............................................ 3
3.陸生植物粒線體基因組已解序之物種 ......................... 3
3.1 粒線體基因組重組和多重結構(multipartite structure) ... 6
3.2 粒線體基因組大小之變異 ............................... 7
3.3 粒線體基因組GC content 和基因組成 ................... 10
3.4 粒線體rRNA 和tRNA 基因 .............................. 11
3.5 粒線體核醣體基因 .................................... 12
3.6 粒線體基因組中參與氧化磷酸化的基因 .................. 13
4.粒線體基因的轉錄 ....................................... 14
5.粒線體基因的轉譯 ....................................... 15
6.粒線體的遺傳特性 ....................................... 17
7.RNA 編輯(RNA editing) ................................. 18
8.粒線體基因組的應用 ..................................... 21
9.粒線體基因組的定序策略 ................................. 22
10.台灣原生種蝴蝶蘭 ...................................... 24
第三章、材料和方法 ....................................... 25
1.實驗材料 ............................................... 25
2.實驗方法 ............................................... 25
2.1 蝴蝶蘭粒線體DNA 的純化 .............................. 25
2.1.1 蝴蝶蘭之來源與處理 .............................. 25
2.1.2 蝴蝶蘭粒線體的純化 .............................. 25
2.1.3 萃取粒線體DNA .................................. 27
2.1.4 RNase A 處理 ................................... 27
2.2 放射性探針雜合高密度膜 ............................. 28
2.2.1 粒線體基因探針的設計 ............................ 28
2.2.2 粒線體基因探針的合成 ............................ 28
2.2.3 BAC clones 高密度膜 ............................. 30
2.2.4 BAC 基因庫篩選 .................................. 30
2.3 篩選含粒線體DNA 片段之BAC colony.................... 32
2.3.1 小量純化BAC DNA ................................ 32
2.3.2 大量純化BAC DNA ................................ 34
2.3.3 Dot-blots 篩選含粒線體DNA 片段的BAC clones ..... 36
2.3.4 BAC colony lifts 製備 ........................... 38
2.4 BAC DNA 特性分析 .................................... 39
2.4.1 脈衝場凝膠電泳(PFGE) ............................ 39
2.4.2 限制片段多型性(RFLP) ............................ 40
2.5 BAC DNA 定序與contigs 排列 .......................... 41
2.6 序列分析 ............................................ 41
2.6.1 BAC DNA 的基因註解 .............................. 41
2.6.2 重複性序列的分析 ................................ 42
2.6.3 轉座子的分析 .................................... 43
2.6.4 RNA 編輯位的預測 ................................ 43
2.6.5 親緣關係樹分析 .................................. 44
第四章、實驗結果 ......................................... 46
1.蝴蝶蘭粒線體DNA 的純化 ................................. 46
2.Genomic BAC libraries 高密度膜雜合的結果 ................ 46
2.1 第一次雜合結果 ...................................... 47
2.2 第二次雜合結果 ...................................... 48
3.篩選含粒線體DNA 之BAC clones ........................... 49
4.脈衝場凝膠電泳(PFGE)分析BAC 的insert size .............. 49
5.利用限制片段多型性(RFLP)做BAC DNA 之fingerprinting ..... 49
6.BAC clones 尾端定序與Blast 結果......................... 50
7.BAC 尾端重疊分析 ....................................... 50
8.BAC 定序結果 ........................................... 51
9.確認BAC 之contigs 排列結果 ............................. 52
10.BAC DNA 片段之基因註解 ................................ 53
11.BAC DNA 片段之重複性序列分析 ........................... 54
12.BAC 片段之轉座子的分析 ................................ 55
13.RNA 編輯位的預測 ...................................... 56
14.姬蝴蝶蘭粒線體基因的親緣關係........................... 57
第五章、討論 ............................................. 58
1.姬蝴蝶蘭粒線體基因組含有來自葉綠體基因組的序列片段 ...... 58
2.姬蝴蝶蘭粒線體基因組 ................................... 58
3.姬蝴蝶蘭粒線體基因組富含重複性序列 ...................... 60
4.姬蝴蝶蘭粒線體基因表現需要RNA 編輯 ...................... 62
5.蝴蝶蘭粒線體基因組的基因 ............................... 63
6.蝴蝶蘭粒線體基因組的應用 ............................... 63
第六章、參考文獻 ......................................... 66
圖目錄
圖一、蝴蝶蘭粒線體DNA 純化後品質之分析 ...................... 81
圖二、使用來自於水稻粒線體基因做為探針之相對位置 ............ 82
圖三、高密度膜示意圖 ..................................... 83
圖四、第一張混合7 種探針雜合姬蝴蝶蘭genomic BAC libraries 高密度膜之結果 .................. 84
圖五、第二張混合7 種探針雜合姬蝴蝶蘭genomic BAC libraries 高密度膜之結果 ................... 85
圖六、第三張混合7 種探針雜合姬蝴蝶蘭genomic BAC libraries 高密度膜之結果 .................. 86
圖七、第四張混合7 種探針雜合姬蝴蝶蘭genomic BAC libraries 高密度膜之結果 .................. 87
圖八、第五張混合7 種探針雜合姬蝴蝶蘭genomic BAC libraries 高密度膜之結果 ................... 88
圖九、第六張混合7 種探針雜合姬蝴蝶蘭genomic BAC libraries 高密度膜之結果 ................... 89
圖十、第一張混合21 種探針雜合姬蝴蝶蘭genomic BAC libraries高密度膜之結果 ................... 90
圖十一、第二張混合21 種探針雜合姬蝴蝶蘭genomic BAC libraries高密度膜之結果 ................. 91
圖十二、第三張混合21 種探針雜合姬蝴蝶蘭genomic BAC libraries高密度膜之結果 ................. 92
圖十三、第四張混合21 種探針雜合姬蝴蝶蘭genomic BAC libraries高密度膜之結果 .................. 93
圖十四、第五張混合21 種探針雜合姬蝴蝶蘭genomic BAC libraries高密度膜之結果 .................. 94
圖十五、第六張混合21 種探針雜合姬蝴蝶蘭genomic BAC libraries高密度膜之結果 ................... 95
圖十六、Dot-blots 篩選含粒線體DNA 片段之BAC clones ......... 96
圖十七、脈衝場凝膠電泳(PFGE)確認39 個可能含有粒線體DNA 片段之 BAC insert size .................... 97
圖十八、39 個BAC clones 之fingerprinting 相似分支情形 ...... 98
圖十九、BAC clones 重疊的結果 ............................. 99
圖二十、BAC-25 contigs 的排列 ........................... 100
圖二十一、BAC-25 限制酵素切位 ............................ 101
圖二十二、限制酵素確認BAC-25 contigs 的排列 ............... 102
圖二十三、BAC DNA 的基因組成示意圖 ........................ 103
圖二十四、BAC DNA 的轉座子分布圖 .......................... 104
圖二十五、姬蝴蝶蘭粒線體rrn18 基因的親緣關係 ............... 105
圖二十六、姬蝴蝶蘭粒線體cob 基因的親緣關係 ................. 106
圖二十七、姬蝴蝶蘭粒線體rpl5 基因的親緣關係 ................ 107
圖二十八、姬蝴蝶蘭粒線體rrn5 基因的親緣關係 ................ 108
圖二十九、姬蝴蝶蘭粒線體rps14 基因的親緣關係 ............... 109
圖三十、姬蝴蝶蘭粒線體rps10 基因的親緣關係 ................. 110
表目錄
表一、已發表在NCBI 資料庫之陸生植物粒線體基因組 ............ 111
表二、本實驗所使用之探針引子 .............................. 112
表三、混合7 個粒線體特異性的基因探針篩選到的姬蝴蝶蘭BAC clones ................................. 114
表四、混合12 個粒線體特異性的基因探針和9 個BAC 端點探針篩選到的姬蝴蝶蘭BAC clones ................. 115
表五、BAC clones 命名與insert size ...................... 116
表六、BAC 尾端定序與Blast 的結果 ......................... 118
表七、34 個BAC 尾端探針與 7 個粒線體特異性的基因探針雜合39個BAC clones 的結果 ..................... 121
表八、BAC 定序的序列組裝結果 .............................. 123
表九、BAC-25 的限制酵素切位 .............................. 124
表十、姬蝴蝶蘭與25 種陸生植物粒線體基因的比較 .............. 125
表十一、BAC DNA 的重複性序列分析 .......................... 126
表十二、BAC DNA 的縱列重複性序列分析 ...................... 127
表十三、BAC DNA 的轉座子序列分析 .......................... 130
表十四、姬蝴蝶蘭粒線體基因可能發生RNA 編輯的位置 ........... 131
附錄
附錄一、藥品與溶液配方 ................................... 133
附表
附表一、454 定序姬蝴蝶蘭DNA 中含有粒線體DNA的67個 contigs ........................................... 137
附表二、454 定序姬蝴蝶蘭DNA 的11 個 contigs 含有BAC-25 和姬蝴蝶蘭葉綠體基因組的序列..................... 143
                                    

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