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研究生:陳鴻大
研究生(外文):Hong Da
論文名稱:演化複製的足跡-基因體的普適等價長度
論文名稱(外文):The Footprint of Evolution Duplication - Universal Equivalent Length of Genomes
指導教授:李弘謙
指導教授(外文):H.C. Paul Lee
學位類別:博士
校院名稱:國立中央大學
系所名稱:物理研究所
學門:自然科學學門
學類:物理學類
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:124
中文關鍵詞:演化RNA世界複製等價長度
外文關鍵詞:EvolutionDuplicationEquivalent LengthRNA word
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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。
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.
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
參考資料
[1] S.L. Miller. A production of amino acids under possible primitive earth con-ditions. Science, 117:528–529, 1953.
[2] J. Or’o. Mechanism of synthesis of adenine from hydrogen cyanide under pos-sible primitive earth conditions. Nature, 191:1193–1194, 1961.
[3] M.R. Walter. Earth‘s earliest biosphere: Its origin and evolution, volume 187-
213. Princeton University Press, 1983.
[4] G.F. Joyce. Rna evolution and the origins of life. Nature, 338:217–224, 1989.
[5] G.F. Joyce. The antiquity of rna based evolution. Nature, 418:214–220, 2002.
[6] L.D. Russell. D.P. Clark. Molecular Biology made simple and fun 2/e. Cache River Press, 2000.
[7] W. K. Johnston and et al. Rna-catalyzed rna polymerization: Accurate and general rna-templated primer extension. Science, 292:1319–1325, 2001.
[8] B. Lewin. Genes VII. Oxford University Press, 2000.
[9] E. Charga.. Structure and function of nucleic acids as cell constituents. Fed. Proc., 10:654–659, 1951.
[10] R. Rudner, J. D. Karkas, and E. Charga.. Separation of b. subtilis dna into complementary strands. iii. direct analysis. Proc. Natl. Acad. Sci. USA, 60:921–922, 1968.
[11] L.C. Hsieh. Universal Lengths of Bacterial Genomes and Model for Genome Growth. PhD thesis, NCU, 2003.
[12] W.H. Li. Molecular Evolution. Sinauer Associates, 1997.
[13] L.F. Lo. Physical aspects on life evolution. Shanghai scienti.c & Technical Publishers, 2000.
[14] Wikipedia.
[15] Ernst Mayr. Biological classi.cation: Toward a synthesis of opposing method-ologies. Science, 214(4520):510–516, 1981.
[16] C R Woese, O Kandler, and M L Wheelis. Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proceed-
ings of the National Academy of Sciences of the United States of America, 87(12):4576–4579, 1990.
[17] C.E. Shannon. A mathematical theory of communication. Bell Sys. Techn. J., 27:379–423, 623–656, 1948.
[18] National center for biotechnology information genome database.
[19] Francis Collins & David Galas. A new .ve-year plan for the u.s. human genome project. Science, 262:43–46, 1993.
[20] David J. Parry-Smith Teresa K. Attwood. Introduction to bioinformatics. Addison Wesley Longman Limited, 2003.
[21] Rice annotation project database.
[22] B-L Hao, H-C Lee, and S-Y Zhang. Fractals related to long dna sequences and complete genomes. Chaos, Solitons and Fractals, 11:825–836, 2000.
[23] C.H. Chang, L.C. Hsieh, T.Y. Chen, H.D. Chen, L.F. Luo, and H.C. Lee. Shannon information in complete genomes. J. Bioinfo. & Comp. Biology, 3:587–608, 2005.
[24] J.W. Fickett, D.C. Torney, and D.R. Wolf. Base compositional structure of genomes. Genomics, 13:1056–64, 1992.
[25] HM Xie and BL Hao. Visualization of k-tuple distribution in procaryote com-plete genomes and their randomized counterparts. In Proceedings of the IEEE Computer Society Bioinformatics Conference, pages 31–42, 2002.
[26] L.S. Hsieh and et al. Minimal model for genome evolution and growth. Phys. Rev. Lett., 90:018101–104, 2003.
[27] H.D. Chen and et al. Divergence and shannon information in genomes. Phys. Rev. Lett., 94:178103, 2005.
[28] C.K. Peng and et al. Mosaic organization of dna nucleotides. Phys. Rev. E, 49:1685–1689, 1994.
[29] P. Bernaola-Galv’an and et al. Study of statistical correlations in dna se-quences. Gene, 300:105–115, 2002.
[30] PW Messer, PF Arndt, and M Lassig. Solvable sequence evolution models and genomic correlations. Phys. Rev. Lett., 94:138103, 2005.
[31] Manolis Kellis, Bruce W. Birren, and Eric S. Lander. Proof and evolutionary analysis of ancient genome duplication in the yeast saccharomyces cerevisiae. Nature, 428(6983):617–624, April 2004.
[32] J. Spring. Genome duplication strikes back. Nature Gen., 31:128–129, 2002.
[33] D. Grant, P. Cregan, and R.C. Shoemaker. Genome organization in dicots:
Genome duplication in arabidopsis and synteny between soybean and ara-bidopsis. Proc. Natl. Acad. Sci. USA, 97:4168–4173, 2000.
[34] P.E. Hansche, V. Beres, and P. Lange. Gene duplication in saccharomyces cerevisiae. Genetics, 88:673–687, 1978.
[35] S. Ohno. Evolution by gene duplication. Springer, New York, 1970.
[36] J. Zhang. Evolution by gene duplication: an update. Trends Eco. Evol., 18:292–298, 2003.
[37] Hubert P. Yockey. Information Theory, Evolution and the Origin of Life. Cambridge University Press, 2005.
[38] A.M. Weiner, P.L. Deininger, and A. Efstratiadis. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse .ow of ge-netic information. Ann. Rev. Biochem., 55:631–661, 1986.
[39] J.M. McGrath, M.M. Jancso, and E. Pichersky. Duplicate sequences with a similarity to expressed genes in the genome of arabidopsis thaliana. Theo. App. Gen., 86:880–888, 1993.
[40] Axel Meyer. Molecular evolution: Duplication, duplication. Nature, 421(6918):31–32, January 2003.
[41] Michael Lynch and John S. Conery. The evolutionary fate and consequences of duplicate genes. Science, 290(5494):1151–1155, 2000.
[42] M. Lynch and A. Force. The probability of duplicate gene preservation by subfunctionalization. Genetics, 154:459–473, 2000.
[43] Chung-I Wu and Chau-Ti Ting. Genes and speciation. Nat Rev Genet, 5(2):114–122, February 2004.
[44] Zhenglong Gu, Lars M. Steinmetz, Xun Gu, Curt Scharfe, Ronald W. Davis, and Wen-Hsiung Li. Role of duplicate genes in genetic robustness against null mutations. Nature, 421(6918):63–66, January 2003.
[45] Albert-Laszlo Barabasi and Zoltan N. Oltvai. Network biology: understanding the cell’s functional organization. Nat Rev Genet, 5(2):101–113, February 2004.
[46] M. Kimura. The neutral theory of molecular evolution. Cambridge Univ. Press, 1983.
[47] Motoo KIMURA. The neutral theory of molecular evolution: A review of recent evidence. The Japanese Journal of Genetics, 66(4):367–386, 1991.
[48] Per Bak, Chao Tang, and Kurt Wiesenfeld. Self-organized criticality: An explanation of the 1/f noise. Phys. Rev. Lett., 59(4):381–384, Jul 1987.
[49] Ge Liu, NISC Comparative Sequencing Program, Shaying Zhao, Je.rey A.
Bailey, S. Cenk Sahinalp, Can Alkan, Eray Tuzun, Eric D. Green, and Evan E. Eichler. Analysis of primate genomic variation reveals a repeat-driven expan-sion of the human genome. Genome Research, 13(3):358–368, 2003.
[50] Tomas Marques-Bonet, Je.rey M. Kidd, Mario Ventura, Tina A. Graves, Ze Cheng, LaDeana W. Hillier, Zhaoshi Jiang, Carl Baker, Ray Malfavon-Borja, Lucinda A. Fulton, Can Alkan, Gozde Aksay, Santhosh Girirajan, Priscillia Siswara, Lin Chen, Maria Francesca Cardone, Arcadi Navarro, Elaine R. Mardis, Richard K. Wilson, and Evan E. Eichler. A burst of seg-mental duplications in the genome of the african great ape ancestor. Nature, 457(7231):877–881, February 2009.
[51] J. A. Bailey and et al. Recent segmental duplications in the human genome. Science, 297:1003–1007, 2002.
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