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研究生:駱冠霖
研究生(外文):Kuan-lin Lo
論文名稱:玉米B染色體的一個特長串聯重複序列的演化
論文名稱(外文):The evolution of a large tandem repeat in the maize B chromosome
指導教授:林伯耀
指導教授(外文):Bor-yaw Lin
學位類別:博士
校院名稱:國立中興大學
系所名稱:分子生物學研究所
學門:生命科學學門
學類:生物科技學類
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:75
中文關鍵詞:玉米B染色體StarkB串聯重複序列
外文關鍵詞:Zea maysB chromosomeStarkBtandem repeat
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為了解玉米B染色體的演化,需要知道B染色體的分子組成。利用微擷取法(microdissection)分離B染色體DNA是可行的方法,但是目前以微擷取法為基礎的篩選流程不足以獲得大量B染色體DNA。為了增加篩選效率,本研究利用一種經DOP-PCR增幅過的探針加以篩選微擷取基因庫(microdissted library),成功獲得59個新的B染色體片段,大部分是高度重複序列,位於B染色體的不同位置,但多數在長臂的異染色質區(heterochromatin)。這些序列同時也存在A染色體上。
玉米B染色體上存在一個特長重複序列StarkB (22.8 kb)。為進一步了解其演化途徑,利用數個B染色體特異性(B-specific)序列,去篩選帶有StarkB的片段。總計獲得18個片段,有九個帶有StarkB內部的序列,另外九個則帶有一段內含兩個彼此串聯(tandem)的StarkB序列。觀察這些篩選的片段中的StarkB,其中的組成單元GrandeB逆轉位子(retrotransposon)皆有相同的標的序列(target sequence),此現象不同於過去對Grande帶有不同標的序列的觀察。另外也觀察到一段內含兩個串聯的StarkB,在南方墨點法(Southern analysis)中表現出強烈的訊號。本研究的眾多觀察指出,與先前研究相反,StarkB應以串聯方式存在。另外一個篩選到的片段,帶有一段與StarkB內的一個組成單元相似的序列,但其結構呈現相反排列,此片段被推測是早期StarkB中,GrandeB尚未轉位(transposition)前的結構。多數的StarkB串聯重複結構,經由不同的外來序列插入(insertion)與序列增幅(amplification)的交替影響,而失去原有的結構。
Understanding the evolution of the maize B chromosome requires insight into the molecular organization of a large number of B clones, which can be potentially obtained by microdissection of the chromosome. Yet, the microdissection protocols currently available are ineffective for a large-scale isolation. In an attempt to improve its efficiency, a protocol was adopted to screen a microdissected B library with probes prepared from the degenerate oligonucleotide primed (DOP)-PCR product of genomic DNA. This protocol resulted in 59 new B clones, most of which were highly repetitive sequences located in various B regions but mostly in the heterochromatic blocks of the long arm. They also appeared in A chromosomes.
A very large repetitive element (StarkB, 22.8 kb) is present in the maize B chromosome. To further understand its evolution, the B-specific fragments were used as probe to isolate the StarkB-carrying sequences. Out of eighteen sequences, nine were the expected internal fragment of StarkB, and nine others were fragments spanning two StarkB elements. One of the two StarkB components, GrandeB, was flanked in all clones with identical target sequences, as opposed to other Grandes that are associated with different target sequences. Also observed was a prominent Southern signal associated with a fragment representing the junction of two adjacent StarkB units. Our results suggest that, contrary to previous assumptions, StarkB organized as tandem arrays. A clone possessing a structure inverse to that of the second component of StarkB is proposed to be the initial element into which a GrandeB inserted to derive StarkB. Most, if not all, isolated StarkB arrays were not the original form, being disrupted by the insertion of various mobile elements intertwined with various stages of amplification.
目次
中文摘要 i
Abstract ii
目次 iii
前言 1
前人研究 2
一、B染色體概論 2
二、B染色體的細胞學形態 2
(一) 菊科植物Brachycome dichromosomatica 3
(二) 菊科植物Crepis capillaris 3
(三) 黑麥(Secale cereal) 3
(四) 玉米(Zea mays) 3
三、B染色體對植物的影響 4
(一) 外表性狀 4
(二) B染色體對A染色體的影響 4
四、B染色體的遺傳特性 5
(一) 不分離(nondisjunction) 5
(二) 優先受精(preferential fertilization) 6
(三) 抑制減數分裂時期的染色體丟失(meiotic loss) 7
五、B染色體的轉錄活性 7
六、B染色體的應用 8
(一) B-A易位染色體(B-A translocation) 8
(二) 人工B染色體(artificial B chromosome) 9
七、B染色體的分子結構 9
(一) Brachycome dichromosomatica 10
1. Brachycome dichromosomatica的large B染色體 10
2. Brachycome dichromosomatica的micro B染色體 10
(二) Crepis capillaris 11
(三) 黑麥(Secale cereal) 12
(四) 玉米(Zea mays) 14
八、B染色體的演化 16
九、基因組中的重複序列 18
十、Grande逆轉位子 19
材料與方法 20
一、植物材料 20
二、微擷取基因庫(microdissected library)的構築與篩選 20
(一) 微擷取基因庫構築 20
(二) 基因庫效價(titer)之測試 20
(三) 基因庫的擴大 21
(四) 嗜菌斑的轉漬 21
(五) 嗜菌斑的南方墨點分析 21
(六) 嗜菌質體(phagemid)的轉型 22
三、基因組DNA之抽取 23
四、B基因組基因庫(genomic library)的構築與篩選 23
(一) 基因組DNA的部分剪切反應 23
(二) 去磷酸化反應 23
(三) 蔗糖連續梯度(sucrose gradient)的製備 24
(四) 超高速離心 24
(五) 基因組基因庫構築 24
(六) 嗜菌體溶出與嗜菌體DNA之抽取 24
五、訊號片段(signaled fragment)之選殖 25
(一) 訊號片段的回收與自我黏合(self ligation) 25
(二) 環形DNA的反向增幅反應(inverse PCR) 25
(三) T-vector的黏合作用 26
(四) 勝任細胞的製作與轉型作用(transformation) 26
六、質體DNA的抽取 27
七、聚合酶連鎖反應(polymerase chain reaction) 27
八、南方墨點法(Southern analysis) 27
(一) 基因組DNA之限制酵素剪切與DNA轉漬 27
(二) 探針的製作 28
(三) 雜合反應 28
(四) 非專一性雜合探針之去除與自動放射顯影 28
九、螢光原位雜合法(Fluorescent in situ hybridization) 29
(一) 粗絲期染色體製備 29
(二) 根尖細胞染色體製備 29
(三) 雜交前的預處理 30
(四) 探針的製作 30
(五) 雜合反應 30
(六) 訊號偵測 30
十、DNA序列分析 31
結果 32
一、自微擷取基因庫(microdissected library)篩選B染色體片段 32
二、 B染色體片段之分析 32
三、以B染色體特異性片段篩選StarkB序列 33
四、分析StarkB上之Grande組成單元 34
五、StarkB在B染色體上的結構 35
六、StarkB的變異 36
七、StarkB的早期結構 38
討論 40
一、B染色體片段的篩選 40
二、B染色體片段的特性 40
三、B染色體起源 41
四、B染色體的串聯重複序列 41
(一) StarkB是一串聯重複序列的證據 41
(二) 其他B染色體上的串聯重複序列 42
(三) StarkB串聯重複序列的序列特性 42
五、StarkB的演化 42
結論 44
一、新的B染色體序列 44
二、新發現的B染色體分子結構 44
三、研究B染色體結構的新策略 44
四、B染色體的演化 45
參考文獻 46


表目次
表1、自基因庫篩選出的新DNA片段的序列分析 58
表2、增幅StarkB各子區域所使用之引子 61
表3、增幅StarkB各子區域所使用之模版 62
表4、Grande的標的序列(5 bp) 63
表5、七個NG次單元的B染色體特異性 64
表6、在南方墨點法分析中,七個L型片段與九個R型片段的訊號強度 65

圖目次
圖1、以南方墨點法分析微擷取B染色體片段 66
圖2、以螢光原位雜合法分析新B染色體片段 67
圖3、比較GrandeB與Grande1-4的分子結構 68
圖4、15個StarkB片段的B染色體特異性 69
圖5、StarkB的串聯重複結構 70
圖6、pBS-3大型序列的結構 71
圖7、以南方墨點法分析StarkB在B染色體上的結構 73
圖8、StarkB的演化模型 74
圖9、比較Grande-rp3與GrandeB的分子結構 75
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