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研究生:許梓亭
研究生(外文):Tzu-Ting Hsu
論文名稱:分析原核生物基因體複製起點與終點的反向對偶對稱現象
論文名稱(外文):Analyzing Inverse Symmetry with Original and Terminal Sites of Prokaryotic Genomes
指導教授:李弘謙
指導教授(外文):Hoong-Chien Lee
學位類別:碩士
校院名稱:國立中央大學
系所名稱:生物資訊與系統生物研究所
學門:生命科學學門
學類:微生物學類
論文出版年:2008
畢業學年度:96
語文別:中文
論文頁數:59
中文關鍵詞:基因體複製原核生物基因體複製終止點複製起始點反向對偶對稱
外文關鍵詞:ReplicationProkaryotic GenomeInverse SymmetryTerminal SiteOriginal Site
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片段複製在基因體的成長與演化上被認為是一個十分重要的機制[1],在酵母菌的染色體上已經證實曾經發生全基因體的複製[2];藉著廣泛地分析許多原核生物,包含 18 個古細菌與 140 個細菌,我們發現一個相當有趣的現象,在這些原核生物的複製起點與終點,有相當顯著的反向對偶對稱性,我們認為在大部分的原核生物曾經發生全基因體的反向對偶複製,這種複製機制發生在複製起點與終點附近;我們利用原核生物的全基因體序列資料,來進行反向對偶對稱性的研究,並且提出證據;不但利用計算鹼基的字串出現頻率來進行分析,還利用同源基因的分佈來觀察驗證;將反向對偶對稱性當作一項特徵,可以應用來預測複製起點與終點的位置;除此之外,藉由比較各種原核生物反向對偶對稱性的差異性,可以將其分成四個種類的類型生物,並且觀察各類型生物和親緣關係樹與系統分類學之間的關係。
Segmental duplication has long been known to be an important mechanism for genome growth and evolution [1]. Beyond that, recent study has spotted occurrence of whole-genome duplication on yeast [2]. In this work we investigate possible association of inverse symmetry with origin sites and terminal sites on genomes. Our findings, through analyses of word-frequency nucleotides and distributions of homologous genes on publicly available complete genomes of 18 archaea and 140 bacteria, are positive. These findings suggest, first, that whole-genome inverse duplications have occurred in most prokaryotic chromosomes near original sites and terminal sites. Secondly, inverse symmetry can be taken as a feature to predict loci of original sites and terminal sites in prokaryotic chromosomes. Thirdly, prokaryotic organisms can be classified into four categories by diversity of inverse symmetry in prokaryotic chromosomes. Phylogeny and taxonomy among the four categories have also been investigated.
中文摘要 ……………………………………………………………… i
英文摘要 ……………………………………………………………… ii
誌謝 ……………………………………………………………… iii
目錄 ……………………………………………………………… iv
一、 簡介………………………………………………………… 1
1-1 查戈夫的宇稱規則………………………………………… 1
1-2 DNA 序列的對稱性………………………………………… 2
1-3 全域對稱與局域對稱……………………………………… 3
1-4 反向對偶對稱與反向對偶複製…………………………… 5
1-5 相關研究…………………………………………………… 7
二、 研究內容與方法…………………………………………… 9
2-1 實驗資料…………………………………………………… 9
2-2 對稱指數定義……………………………………………… 9
2-3 基因體分類公式…………………………………………… 13
三、 結果………………………………………………………… 17
3-1 反向對偶對稱指數應用於基因體的複製起點與終點…… 17
3-2 基因體正股與反股的同源基因分布與反向對偶對稱現象 19
3-3 物種分類函式和物種親緣關係樹和系統分類學的關係… 26
四、 討論………………………………………………………… 33
五、 參考文獻…………………………………………………… 35
六、 附錄………………………………………………………… 37
附錄A 原核生物的反向對稱、對偶對稱與反向對偶對稱指數… 38
附錄B 原核生物的物種資料……………………………………… 46
附錄C 原核生物分類情形和複製起點與終點的位置…………… 53
[1] Lynch M. Genomics. Gene duplication and evolution. (2002) Science 297:945-7.
[2] Wolfe, KH, DC. Molecular evidence for an ancient duplication of the entire yeast genome. (1997) Nature 387:708-13.
[3] Forsdyke DR, Mortimer JR. Chargaff''s legacy. (2000) Gene 261:127-37.
[4] Chargaff E. Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. (1950) Experientia 6:201-9.
[5] Chargaff E. Structure and function of nucleic acids as cell constituents. (1951) Fed Proc. 10:654-9.
[6] Watson JD, Crick FH. Genetical implications of the structure of deoxyribonucleic acid (1953) Nature 171:964-7.
[7] Rudner R, Karkas JD, Chargaff E. Separation of B. subtilis DNA into complementary strands, I. Biological properties (1968) Proc. Natl. Acad. Sci. U S A. 60:630-5.
[8] Perna NT, Kocher TD. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. (1995) J Mol Evol. 41:353-8.
[9] Grigoriev A. Analyzing genomes with cumulative skew diagrams. (1998) Nucleic Acids Res. 26:2286-90.
[10] Sanchez J, Jose MV. Analysis of bilateral inverse symmetry in whole bacterial chromosomes. (2002) Biochem Biophys Res Commun. 299:126-34.
[11] Song J, Ware A, Liu SL. Wavelet to predict bacterial ori and ter: a tendency towards a physical balance. (2003) BMC Genomics 4:17.
[12] Mackiewicz P, Zakrzewska-Czerwinska J, Zawilak A, Dudek MR, Cebrat S. Where does bacterial replication start? Rules for predicting the oriC region. (2004) Nucleic Acids Res. 32:3781-91.
[13] Zhang R, Zhang CT. Identification of replication origins in archaeal genomes based on the Z-curve method. (2005) Archaea 1:335-46.
[14] Gao F, Zhang CT. DoriC: a database of oriC regions in bacterial genomes. (2007) Bioinformatics 23:1866-7.
[15] Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. (2004) Bioinformatics 20:3682-6.
[16] Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW. Origin of replication in circular prokaryotic chromosomes. (2006) Environ Microbiol. 8(2):353-61.
[17] Necsulea A, Lobry JR. A new method for assessing the effect of replication on DNA base composition asymmetry. (2007) Mol Biol Evol. 24:2169-79.
[18] Chen HD, Chang CH, Hsieh LC, Lee HC. Divergence and Shannon information in genomes. (2005) Phys Rev Lett. 94:178103.
[19] Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. (1997) Science 278:631-7.
[20] Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated version includes eukaryotes. (2003) BMC Bioinformatics 4:41.
[21] Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. (2006) Science 311:1283-7.
[22] Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. (2007) Bioinformatics 23:127-8.
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