基因體中的倒位對稱及全基因體的倒位複製

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康星源(Sin-Guan Kong) 查詢紙本館藏

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物理學系

論文名稱

基因體中的倒位對稱及全基因體的倒位複製
(Inverse symmetry in genomes and whole-genome inverse duplication)

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摘要(中)

片段複製長久以來被當作基因體成長及演化的重要機制[40,57]，最近確實了全基因體複製的確發生在酵母菌[50]及一些硬骨魚種類當中[53-54]。在這裡，我們提供了證據證明全基因體的倒位複製非常可能發生在至少一半的真細菌當中，更甚至絕大部份的染色體裡。我們研究了現有資料庫提供的染色體的倒位對稱並從中得到了證據。發現了絕大部份的染色體都擁有全域的倒位對稱，但在局部上的倒位對稱卻有幾種不同的樣式。這些樣式為倒位對稱的片段複製發生在基因體中的統一論述提供了線索。

摘要(英)

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.

關鍵字(中)

★ 基因體複製
★ 倒位對稱

關鍵字(英)

★ duplication
★ inverse symmetry

論文目次

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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指導教授

李弘謙(Hoong-Chien Lee)

審核日期

2008-7-10

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