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Student Number 92242006
Author Sin-Guan Kong(康星源)
Author's Email Address No Public.
Statistics This thesis had been viewed 1497 times. Download 379 times.
Department Physics
Year 2007
Semester 2
Degree Ph.D.
Type of Document Doctoral Dissertation
Language zh-TW.Big5 Chinese
Title Inverse symmetry in genomes and whole-genome inverse duplication
Date of Defense 2008-07-04
Page Count 71
Keyword
  • duplication
  • inverse symmetry
  • Abstract Segmental duplication has long been known to be an important mechanism for genome growth and evolution [40,57], and recently it has been firmly established that whole-genome duplications have at least occurred in yeast [50] and in some species of fishes ray-finned fishes [53-54]. Here we present evidence showing that whole-genome inverse duplication very likely occurred in one half of eubacterial genomes, and possibly in most chromosomes, prokaryotic as well as eukaryotic. We derive our evidence through a comprehensive study of the inverse symmetry in all publicly available complete genomes. We find that a vast majority of chromosomes have close to maximum global inverse symmetry, but the chromosomes exhibit starkly distinct patterns of local inverse symmetry. These patterns provide clues for a consistent narrative of the many ways inverse segmental duplications may have occurred in genomes.
    Table of Content 英文摘要---------------------------------------------------------------------------------------------------i
    中文摘要--------------------------------------------------------------------------------------------------ii
    誌謝--------------------------------------------------------------------------------------------------------iii
    目錄--------------------------------------------------------------------------------------------------------iv
    圖目錄-----------------------------------------------------------------------------------------------------vi
    表目錄----------------------------------------------------------------------------------------------------vii
    第一章簡介-------------------------------------------------------------------------------------------1
    1.1從Chargaff的宇稱規則談起-------------------------------------------------------1
    1.2鹼基對偶對稱指數(Base-complement symmetry index)介紹-------------2
    1.3全域及局部對稱指數(Symmetric indices)簡介-------------------------------2
    1.4鹼基扭曲方法簡介-------------------------------------------------------------------4
    1.5單鹼基扭曲的延伸-多鹼基扭曲簡介-----------------------------------------6
    第二章實驗方法及材料---------------------------------------------------------------------------8
    2.1 字串出現頻率及配分---------------------------------------------------------------8
    2.2 鹼基對偶對稱指數的定義-------------------------------------------------------10
    2.3 對稱指數的定義--------------------------------------------------------------------11
    2.4 局部的倒位對稱分析-------------------------------------------------------------12
      2.4.1 不同尺度下的平均倒位對稱指數------------------------------------12
      2.4.2倒位對稱矩陣---------------------------------------------------------------13
      2.4.3 的滑動掃瞄--------------------------------------------------------------14
      2.4.4 以ori及ter為中心的 掃瞄------------------------------------------14
    2.5 單鹼基及多鹼基的扭曲----------------------------------------------------------14
    2.6 實驗材料------------------------------------------------------------------------------15
    2.7 程式碼---------------------------------------------------------------------------------16
    第三章結果------------------------------------------------------------------------------------------17
    3.1 鹼基對偶對稱指數----------------------------------------------------------------17
    3.2 對稱指數------------------------------------------------------------------------------19
    3.3 局部的對稱指數--------------------------------------------------------------------24
      3.3.1 在不同尺度下的局部對稱指數---------------------------------------24
      3.3.2 倒位對稱矩陣圖-----------------------------------------------------------31
      3.3.3 倒位對稱指數掃瞄-------------------------------------------------------34
      3.3.4 以ori及ter為中心的掃瞄---------------------------------------------36
    3.4 累積的單鹼基及多鹼基扭曲---------------------------------------------------39
      3.4.1 CIR是累積的單及多鹼基扭曲的轉折點---------------------------39
      3.4.2對偶及反向扭曲的大小是普適的並與分類無關-----------------41
      3.4.3倒位對稱扭曲與局部倒位對稱呈負相干關係 -------------------41
    第四章討論------------------------------------------------------------------------------------------42
    4.1 鹼基對偶對稱指數----------------------------------------------------------------42
    4.2 對稱指數------------------------------------------------------------------------------44
      4.2.1 對稱指數方法上的比較-------------------------------------------------44
      4.2.2 倒位對稱在基因體中的證實------------------------------------------45
      4.2.3 倒位對稱矩陣的啟發----------------------------------------------------47
         4.2.3.1 倒位對稱因倒位對稱複製造成----------------------------47
         4.2.3.2 A類型暗示著如染色體般全長的複製---------------------47
         4.2.3.3 D類型暗示著發生過許多prox-ISD事件------------------49
         4.2.3.4對於所有類型的統一詮釋------------------------------------49
    4.3 鹼基扭曲與倒位對稱的關聯---------------------------------------------------50
    4.4倒位對稱複製及染色體複製-----------------------------------------------------53
    第五章結論、推測結論及未來展望---------------------------------------------------------54
    5.1 鹼基對偶對稱指數----------------------------------------------------------------54
    5.2全基因體的對稱指數--------------------------------------------------------------55
    5.3局部的倒位對稱指數--------------------------------------------------------------55
    5.4單或多鹼基扭曲-------------------------------------------------------------------57
    5.5未來展望------------------------------------------------------------------------------58
    參考文獻------------------------------------------------------------------------------------------------59
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    Advisor
  • Hoong-Chien Lee(李弘謙)
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    Date of Submission 2008-07-10

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