基因體結構改變於細菌與病毒演化之影響｜國立清華大學博碩士論文庫

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研究生：	林介華 Lin, Chieh Hua
論文名稱：	基因體結構改變於細菌與病毒演化之影響 The Influences of genomic structural alternations on the evolution of bacterial and viral genomes
指導教授：	熊昭 Hsiung, Chao A 呂平江 Lyu, Ping Chiang
口試委員:	熊昭 Hsiung, Chao A 呂平江 Lyu, Ping Chiang 陳豐奇 Chen, Feng Chi 林仲彥 Lin, Chung Yen 林勇欣 Lin,YeongShin
學位類別：	博士 Doctor
系所名稱：	生命科學暨醫學院 - 生物資訊與結構生物研究所 Institute of Bioinformatics and Structural Biology
論文出版年：	2015
畢業學年度：	103
語文別：	英文
論文頁數：	191
中文關鍵詞：	演化速度、轉錄方向、腸病毒、基因型鑑定、基因重組
外文關鍵詞：	evolutionary rates, transcriptional orientation, enterovirus, genotyping, recombination
相關次數：	點閱：3 下載：0
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細菌與病毒基因體之演化速率快，乃源自於在短暫且快速的生長複製周期，容易發生累積較多的突變事件，並且頻繁的發生基因結構改變；但目前對於基因結構改變是否會影響基因序列的替換率，以及其相關機制仍未臻明確，本論文分別著眼於細菌與病毒基因體內基因結構改變對基因演化速率之影響。在本論文第二章，我們針對腸道細菌基因體在演化過程中轉錄方向發生變化的基因，量測其演化速率，進一步暸解細菌基因的轉錄方向改變究竟是受到突變或是天擇作用所趨動。研究結果顯示，當基因轉錄方向改變後，同義替換率(synonymous substitution, dS)和非同義替換率(non-synonymous substitution, dN)皆有提高，但是與轉錄方向無變化的基因相比，非同義與同義替換率之間的比例 (dN/dS)則無顯著差異，由此可推測細菌基因的轉錄方向改變的趨動力可能主要來自於突變作用。為確認基因轉錄方向改變所造成的演化速度提升是否受到其他因子所影響，我們控制數個已知會影響演化速率的因子，包括是否為必要性基因、基因表現量多寡、複製與轉錄機制的作用方向是否衝突、以及基因座落於基因體的位置相距複製原點/終點之距離，以上結果均顯示轉錄方向改變的基因，其dN和dS速率加快的原因只與轉錄方向改變有關，且受到突變作用所趨動。
在本論文第三章，主要預定目標在於探討基因重組在病毒基因體演化以及致病力所造成的影響和改變，欲達成此目標，需使用不同基因片段對病毒序列進行型別鑑定，但目前現有的型別鑑定工具僅只有使用外殼蛋白，故我們在開始進行此預定目標研究之前，建立了一個可用於腸病毒基因型鑑定與偵測基因重組事件的線上分析工具(EVIDENCE)；同時，為了排除由於基因型鑑別方法不同或是只使用部份序列進行基因型鑑別，而導致錯誤的型別鑑定結果，我們結合BLAST結果中的三個參數：序列相似度、涵蓋率與BLAST得分，將其轉換為名次後加總，用此”混合式排名法＂(mixed–ranking scores)來對GenBank中所有的腸病毒序列重新分類，此一重新分類結果有助於未來進行後續研究時，可先行排除被分類於錯誤型別的序列資料。此研究所發展出的基因定型與基因重組偵測工具，能有效加速未來於腸病毒演化之相關研究。

Prokaryotic and viral genomes evolve rapidly by high mutation rates and frequent genomic structural changes, including recombination, gene gain/loss and genome rearrangement. However, whether and how genomic structural alterations might influence the substitution rates of prokaryotic genes remains underexplored.
In Chapter 2, we examine the correlations between evolutionary rates and changes in transcriptional orientation in enterobacterial genomes. Our results indicate that changed-orientation genes (ChOGs) have significantly higher rates of synonymous (dS) and non-synonymous (dN) substitutions but similar dN/dS ratios as compared with same-orientation genes (SOGs). The correlations are not confounded by gene essentiality, gene expression level, replication-transcription confrontation, or genomic location. These observations suggest that the increases in evolutionary rates in ChOGs may be mainly mutation-driven instead of selection-driven.
In Chapter 3, we aim to investigate the effects of genomic recombination on the evolution of viral genes. As the first step, we develop a web-based tool for Enterovirus (EV) genotyping and recombination detection named EVIDENCE (Enterovirus in deep conception). Additionally, to avoid potential mistyping, we introduce the “mixed–ranking scores” to evaluate the fitness of prototypes by the relatedness and by the genome regions of interest. The mixed-ranking scores which sum up the rank of three parameters in BLAST result, including identity, query coverage and bit-score, were used in genotype re-classification and the first step of novel sequence genotyping to overcome inherent disadvantage for using each of them alone. This platform can facilitate future studies in EV evolution.

論文指導教授推薦書
學位考試委員會審定書
誌謝
中文摘要    I
ABSTRACT    III
Chapter 1. INTRODUCTION    1
Chapter 2. Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes    5
2.1 Introduction    5
2.2 Methods    7
2.2.1 Data sources    7
2.2.2 Estimation of evolutionary rates and statistical analyses    8
2.2.3 Analysis of gene expression data    9
2.2.4 Functional enrichment analysis    9
2.3 Results and Discussion    10
2.3.1 ChOGs have higher dN and dS but similar dN/dS ratio when compared with SOGs    10
2.3.2 Confounding factor 1: Gene essentiality    10
2.3.3 Confounding factor 2: Gene expression level    11
2.3.4 Confounding factor 3: Background mutation rate    12
2.3.5 Confounding factor 4: Replication–transcription confrontation    12
2.3.6 Confounding factor 5: Decreased dS at gene terminals (codon usage bias)    13
2.3.7 Functional enrichment analysis of ChOGs    14
2.4 Conclusions    14
Chapter 3. Enterovirus Genotyping: Current Problems and a Potential Solution    16
3.1 Introduction    16
3.2 Material and methods    18
3.2.1 Reference Sequence Sets    18
3.2.2 A mixture-ranking score of BLAST-based genotyping method    19
3.2.3 Phylogenetic-based genotyping procedure    21
3.2.4 Recombination detection    22
3.2.5 Implementation    23
3.3 Results and Discussion    24
3.3.1 Statistics of GTRefSet and ExtRefSet    24
3.3.2 Updating the classification of sequences using BLAST-based genotyping method    24
3.3.3 Modulized phylogenetic-based genotyping    26
3.3.4 Recombination    27
3.3.5 A case study    28
3.3.6 The value-added function of EVIDENCE    30
3.4 Conclusion    31
Chapter 4. CONCLUSION and LIMITATION    32
Chapter 5. FURTHER WORK    33
Figures
Figure 1. The evolutionary rates of ChOGs and SOGs in the ECO-KPN and STM-KPN comparisons.    46
Figure 2. The evolutionary rates of ChOGs and SOGs in the ECO-KPN and STM-KPN comparisons.    47
Figure 3. The evolutionary rates in (a) ECO-KPN comparison; and (b) STM-KPN comparison.    49
Figure 4. Comparison of the evolutionary rates of highly and non-highly expressed ChOGs.    50
Figure 5. Dot plot for the analyzed orthologous genes in the (a) ECO-KPN; and (b) STM-KPN comparison.    51
Figure 6. The evolutionary rates of ChOGs and SOGs that are subject to head-on collision or co-orientation between DNA replication and transcription in the ECO-STM comparison.    52
Figure 7. Difference in evolutionary rates between the terminal and middle region of (a) ECO-KPN and (b) STM-KPN orthologous genes.    53
Figure 8. The Genotype re-classification procedures    54
Figure 9. EVIDENCE interface.    56
Figure 10. Statistics of GTRefSet.    57
Figure 11. Recombination detection of a high virulent enterovirus strain CA16/GD09/119.    58
Figure 12. Recombination detection of a mild virulent enterovirus strain CA16/GD09/24.    59
Tables
Table 1. The numbers of the orthologous gene pairs analyzed in this study.    60
Table 2. (a) The total numbers of orthologous gene pairs identified by reciprocal BLASTP and the OMA database. (b) The numbers of ECO-KPN, ECO-STM, and STM-KPN orthologous gene pairs identified by both mthods.    61
Table 3. The numbers of ChOGs with dS > 3 in the ECO-KPN, ECO-STM, and STM-KPN comparisons.    62
Table 4. The median evolutionary rates of ChOGs and SOGs when different confounding factors are controlled.    63
Table 5. Distance from Ter in ChOGs of ECO and STM    64
Table 6. Partial correlations between evolutionary rates and the ChOG/SOG gene type while the physical distance from Ter is controlled.    65
Table 7. Functional enrichment analyses for ChOGs in the (a) ECO-KPN and (b) ECO-STM comparisons.    66
Table 8. Congruence of species assignment in GenBank and EVIDENCE    69
Table 9. Briefs of sequences newly assigned to the EV-A71 genotype following the re-classification procedures.    70
Table 10. Validation Dataset    71
Appendix Tables
Appendix Table 1 : The detailed information of the orthologous gene pairs analyzed in this study.    72
Appendix Table 2. GTRefSet list. The reference sequences used in genotyping, with ICTV formal acronym, GenBank accession number of sequenced region.    127
Appendix Table 3. ExRefSet list. The reference sequences used in re-classification, with ICTV formal acronym, GenBank accession number and sequenced region. These starins were integrated GTRefSet into ExRefSet.    137
Appendix Table 4. Summary of congruence between GenBank and re-classification in this study.    151
Appendix Table 5. Lists of comparison sets in genera Mycoplasma (A), Mycobacterium (B) and Vibrio (C).    166

                                

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