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研究生:王翔昱
研究生(外文):Wang, Hsiang-Iu
論文名稱:相似短序列比對工具於多組分單鏈去氧核糖核酸病毒演化分析之應用
論文名稱(外文):Application of Motif-Based Tools on Evolutionary Analysis of Multipartite Single-Stranded DNA Viruses
指導教授:唐傳義
指導教授(外文):Tang, ChuanYi
學位類別:博士
校院名稱:國立清華大學
系所名稱:資訊工程學系
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2014
畢業學年度:102
語文別:英文
論文頁數:59
中文關鍵詞:相似短序列多組分病毒病毒演化重組親源分析香蕉束頂病毒
外文關鍵詞:MoitifMultipartite virusVirus EvolutionRecombinationPhylogenetic analysisBanana bunchy top virus
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多組分病毒 (multipartite viruses) 的基因體包含了一個以上、且序列相異的基因體單元 (genome component),這種病毒被認為是演化自只具有單一基因體單元的野生種病毒。為了探討基因體重組 (recombination) 在多組分病毒的演化中扮演的角色,我們發展了以相似短序列比對工具為基礎 (motif-based) 的系統性策略,在多組分病毒的非相似序列中找尋相似短序列,並且採取統計策略從中選取可信度高、亦即可能具有生物意義的短序列進行分析,以此策略進行分析所獲得的資訊,提供了更多關於病毒演化的資訊。本研究比較了以相似短序列為基礎的此種策略與以序列對位比對 (alignment-based) 為主的傳統分析方式,並且將此策略實際運用於分析多組分單鏈去氧核糖核酸病毒,包括菜豆金色黃花葉病毒屬 (Begomovirus) 中所有的雙組分病毒、具有六個基因體單元的香蕉束頂病毒 (Banana bunchy top virus, BBTV) 以及具有八個基因體單元的蠶豆壞死黃化病毒 (Faba Bean Necrotic Yellows Virus, FBNYV)。本研究的分析結果顯示,基因體重組現象不僅發生在某些菜豆金色黃花葉病毒屬的兩個基因體單元之間,也發生在香蕉束頂病毒與蠶豆壞死黃化病毒的基因體中。分析資料同時也發現,許多不尋常的基因體重組事件促進了香蕉束頂病毒不同基因單元之間的演化。
Multipartite viruses contain more than one distinctive genome component, and the origin of multipartite viruses has been suggested to evolve from a non-segmented wild-type virus. To explore whether recombination also plays a role in the evolution of the genomes of multipartite viruses, we developed a systematic approach that employs motif-finding tools to detect conserved motifs from divergent genomic regions and applies statistical approaches to select high-confidence motifs. The information that this approach provides helps us understand the evolution of viruses. In this study, we compared our motif-based strategy with current alignment-based recombination-detecting methods and applied our methods to the analysis of multipartite single-stranded plant DNA viruses, including bipartite begomoviruses, Banana bunchy top virus (BBTV) (consisting of 6 genome components) and Faba bean necrotic yellows virus (FBNYV) (consisting of 8 genome components). Our analysis revealed that recombination occurred between genome components in some begomoviruses, BBTV and FBNYV. Our data also show that several unusual recombination events have contributed to the evolution of BBTV genome components. We believe that similar approaches can be applied to resolve the evolutionary history of other viruses.
Chapter 1 Introduction ................................................................................................... 2
1.Multipartite Viruses ................................................................................................... 2
2.Current recombination detection motif ................................................................... 3
3.Motifs ........................................................................................................................... 4
4.Contribution ........................................................................................................ 5
Chapter 2 Result ............................................................................................................. 6
1. Comparison of recombination detection methods ................................................ 6
2. Identification of motifs of bipartite begomoviruses .............................................. 9
3. Application of motif-based analysis to BBTV .................................................... 14
4. Phylogenetic analysis of BBTV ............................................................................ 21
5. Motif distribution of BBTV ................................................................................... 25
6. Application of motif-based analysis to FBNYV ................................................. 27
Chapter 3 Discussion ................................................................................................... 29
Chapter 4 Metarial and Methods .................................................................................. 35
1. Sequences used in this study .................................................................................. 35
2. Alignment, rearrangement, distance calculation, phylogenetic analysis and
recombination seeking ............................................................................................ 35
3. The construction of the virus-genome mimic sequence set ............................... 36
4. Motif detection and measurement of similarity ................................................... 38
5. Simulation data construction for threshold determination ................................. 40
Chapter 5 Supporting information ................................................................................. 42
1. Supporting table ...................................................................................................... 42
2. Supporting figures .................................................................................................. 48
Bibliography ........................................................................................................................ 54
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