演化複製的足跡 - 基因體的普適等價長度

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姓名

陳鴻大(Hong Da) 查詢紙本館藏

畢業系所

物理學系

論文名稱

演化複製的足跡 - 基因體的普適等價長度
(The Footprint of Evolution Duplication - Universal Equivalent Length of Genomes)

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摘要(中)

複製事件廣泛存在基因體的歷史當中，主導了基因序列的成長與演化。為了比較不同基因體間複製演化的共同特性，我們定義了序列的等價長度 l_e，等度價長度的直接意義即是，這個序列與長度 l_e 的隨機序列具有"等價的隨機性質"。也就是說，隨機序列的等價長度即等於自身的序列長，等價長度會在序列遭受隨機突變時增長，而在序列被複製時保持不變。
根據我們的研究，基因體具有普世的等價長度，且在染色體不同部分的等價長度皆相同，顯示原始的基因序列可能開始於一短序列，經由隨機片段複製作為演化動力而成長。這個結論與 RNA 世界假說相符合，而且能夠解釋存在先今基因體當中頻密的複製事件，或許也可為演化速率不平均的爭議提供解答。

摘要(英)

Segmental duplication is widely held to be a dominant feature in the dynamics of
genome growth and evolution. Yet how this would a ect the global structure of
genomes has not been discused. Here, we identify the equivalent length, Le, of a
genomic sequence as a medium through which that dominance may be discussed
quantitatively. Through examining 865 complete chromosomes we nd the Le for a
genomic sequence to be nearly invariant and remarkably short compared true sequence
length { in terms of the statistics of two-letter words it is about 300 bases long { and
is approximately universal for all (examined) complete chromosomes. We verify this
result to be non-trivial, in particular, not caused by the similarity of sequences in
any commonly held sense, and demonstrate that it is easy to generate genome-like
sequences not having universal Le’’s. We establish a causal relation between short
Le and segmental duplication and show that a simple, random-segmental-duplication
driven model for genome growth generates highly diverse genome-like sequences that
have universal Le’’s. We postulate a connection between the universal value of Le and
maximum information capacity in genomic sequences and infer that the universality of
Le is a crucial product of the evolution of genome toward maximum tness.

關鍵字(中)

★ 演化
★ RNA世界
★ 複製
★ 等價長度

關鍵字(英)

★ Evolution
★ Duplication
★ Equivalent Length
★ RNA word

論文目次

目錄
序 iii
致謝 iv
摘要 v
Abstract vi
1緒論 1
1.1生物訊息的載體 .............................. 1
1.1.1生命的起源 ............................ 1
1.1.2基因序列的構造 .......................... 2
1.2基因序列的演化模式 ........................... 4
1.2.1基因序列的突變與重組 ...................... 4
1.2.2自然選擇與物種分類 ....................... 5
1.3隨機系統的特性 .............................. 7
1.3.1隨機的定義 ............................ 7
1.3.2中央極限定理 ........................... 7
2材料與方法 9
2.1基因序列資料的來源 ........................... 9
2.1.1基因體計畫與資料庫 ....................... 9
2.1.2基因序列的內容 .......................... 10
2.2字串分佈的統計分析 ........................... 11
2.2.1寡核甘酸頻率法 .......................... 11
2.2.2變異係數與隨機背景 ....................... 11
2.3序列的等價長度 .............................. 13
2.3.1等價長度的定義與特性 ...................... 13
2.3.2熵與 Shannon資訊 ....................... 14
vii
目錄
3研究結果 15
3.1等價長度的普適性 ............................. 15
3.1.1基因體與隨機序列的等價長度 ................... 15
3.1.2不同物種的等價長度 ....................... 18
3.2等價長度的分佈 .............................. 22
3.2.1等價長度的普適公式 ....................... 22
3.2.2編碼與非編碼序列的等價長度 ................... 22
3.3隨機化序列的等價長度 .......................... 24
3.3.1突變序列的等價長度 ....................... 24
3.3.2複製序列的等價長度 ....................... 26
4討論 29
4.1等價長度的生物意涵 ........................... 29
4.1.1隨機片段複製 ........................... 29
4.1.2熵的維持 ............................. 30
4.2複製的演化優勢 .............................. 30
4.2.1基因型的多樣性 .......................... 30
4.2.2表現型的穩定性 .......................... 30
4.3新達爾文主義的困惑 ........................... 30
4.3.1基因漂變與中性論 ......................... 30
4.3.2疾變平衡的演化速率 ....................... 31
參考資料 32
A附表 36
A.1基因序列表 ................................ 36
A.2等價長度表 ................................ 53
viii
圖目錄
1.1 DNA與 RNA構造示意圖 ........................ 3
1.2物種分類的系統發生樹 .......................... 6
2.1基因體與其隨機相似序列的字串頻率分佈 ................. 12
3.1變異系數的震盪項與非震盪項對鹼基比例作圖 ............... 16
3.2基因體序列與隨機序列中不同片段的等價長度比較 ............. 17
3.3等價長度對基因序列長及鹼基比例作圖 .................. 19
3.4對完整基因體序列的平均等價長度 ..................... 19
3.5等價長度的擬合曲線 ........................... 23
3.6鹼基比例對編碼區及非編碼區平均等價長度的影響 ............. 23
3.7點突變次數對基因體等價長度的影響 ................... 25
3.8隨機化序列中等價長度的尺度 ....................... 26
ix
表目錄
3.1不同鹼基比例對基因序列及隨機序列的變異係數 .............. 16
3.2基因體字串出現頻率分佈的 P-values ................... 18
3.3不同物種分類的等價長度 ......................... 20
3.4各種模式生物的等價長度 ......................... 21
3.5高度偏斜鹼基組成的部分染色體等價長度 ................. 24
3.6鹼基比例及編碼與非編碼區的等價長度比 ................. 25
3.7不同複製序列的等價長度 ......................... 27
3.8連鎖序列的等價長度 ........................... 27
A.1原核生物序列表 .............................. 36
A.2單細胞生物序列表 ............................. 44
A.3昆蟲序列表 ................................ 46
A.4植物序列表 ................................ 47
A.5脊椎動物序列表 .............................. 47
A.6原核生物等價長度表 ........................... 53
A.7 Unicell Le (106). ............................. 77
A.8 Le of Insects (39). ............................ 86
A.9 Le of Plant (17). ............................. 89
A.10 Le of Vertebrates (236). ......................... 91

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指導教授

李弘謙(H.C. Paul Lee)

審核日期

2009-7-31

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