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研究生:黃煜婷
研究生(外文):Yu-Ting Huang
論文名稱:烏魚磷酸葡萄糖異構酶的基因體結構及磷酸葡萄糖異構酶在真核生物的演化
論文名稱(外文):Genomic Structures of Gray Mullet Phosphoglucose Isomerases (PGI), with Reference to PGI Evolution in Eukaryotes
指導教授:高孝偉高孝偉引用關係
學位類別:碩士
校院名稱:國立中興大學
系所名稱:生命科學系所
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2007
畢業學年度:95
語文別:英文
論文頁數:97
中文關鍵詞:外顯子內隱子親緣關係樹
外文關鍵詞:exonintronphylogenetic tree
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內隱子是存在於基因中的DNA序列,它會在mRNA轉錄過程中被移除。真核生物基因具有內隱子,但是古生菌和細菌則無內隱子。有關真核生物內隱子的起源及演化的問題有兩種假說,即introns-early 和introns-late模式。Introns-early模式認為內隱子早就存在於真核生物、太古菌及細菌共同祖先的基因體中。太古菌與細菌的基因體中無內隱子是因為後來失去內隱子。Introns-late模式則認為所有存在於真核生物基因體的內隱子皆為後來插入的。近來學者則提出了綜合模式,認為內隱子會在不同支系物種的基因體中發生插入和失去的事件。早就存在的內隱子被稱為古內隱子(ancient intron)。古內隱子必須符合三個條件,即(1)此內隱子必須是屬於phase-0、(2)其位置各物種支系中必須是保守的、(3)必須介於蛋白質模組之間。磷酸葡萄糖異構酶 (Phosphoglucose isomerase,以下簡稱PGI)是一種糖類代謝酵素,並廣泛存在於真核生物、太古菌和細菌中。雖然有些植物、昆蟲和哺乳類的PGI基因體結構已經被確定,但是真骨魚類PGI的基因體結構還沒有報告發表。過去研究中指出真骨魚類具有兩個PGI基因座(PGI-A和PGI-B),但是基因複製的機制尚未確定。在本研究中,以聚合酵素鏈鎖反應方法增幅烏魚的PGI-A和PGI-B 之基因體序列並將其定序。另外也從GenBank和Ensembl資料庫中擷取其他兩種真骨魚類的PGI cDNA和基因體序列一起做分析。結果顯示真骨魚的兩個PGI 基因座是同源的,而其基因複製是經由染色體多倍體化的機制。為了推論PGI內隱子及PGI胺基酸序列的演化,自Genbank和Ensembl資料庫中擷取其他真核生物的PGI cDNA和基因體序列。以上述三種條件來判斷,顯示真核生物PGI的基因體中無古內隱子,因此不支持introns-early 模式。以最大簡約法分析推論PGI內隱子的演化,顯示真核生物PGI的內隱子都是後來插入的,而有些內隱子則會在演化過程中失去。以PGI 胺基酸序列和基因體資料重建親緣關係樹,結果並不能完全顯示真核生物的親緣關係,可能是由於趨同演化及缺少衍徵所造成的結果。以PGI內隱子序列做為分子標誌來推論三種鯔科魚類(烏魚、大鱗鮻魚和白鮻魚)的種間及其種內的親緣關係,結果發現此分子標誌可以解析種間的親緣關係但無法完全解析種內的親緣關係。
Introns are segments of genes that are removed when the primary transcript is processed to give the mature mRNA. Eukaryotes are characterized by the presence of introns, whereas archaebacteria and eubacteria are characterize by the absence of introns. There are two competing models for the origin of introns: introns-early models and introns-late models. The introns-early models propose that introns arose before the divergence of eukaryotes, archaebacteria, and eubacteria, but introns were lost from archaebacteria and eubacteria. The introns-late models advocate that introns were inserted into eukaryotic genomes after the divergence of eukaryotes, archabacteria, and eubacteria. Recent studies suggest mixed models of introns early and late that introns have been gained and lost in different eukaryotic lineages. Three criteria are used to identify the ancient introns. (1) The ancient intron should be phase-0, (2) it exits in major lineages of eukaryotes, and (3) lays between protein modules. Phosphoglucose isomerase (PGI) is an enzyme involved in glycolysis and gluconeogenesis and present in eukaryotes, archaebacteria, and eubacteria. Although PGI genomic structures of plant, insect, and mammals have been determined, there was no published paper about fish PGI genome. Previous studies suggest that teleost fishes have two PGI loci (PGI-A and PGI-B). However, the mechanism of gene duplication is not conclusive. In the present study, PGI-A and PGI-B genomic structures of gray mullet were determined using polymerase chain reaction. In addition, PGI cDNA and genomic sequences of two additional teleost fish were also retrieved from GenBank and Ensembl and analyzed. The results support that the duplicated PGIs of the teleost fishes were homologous and the duplication was through the mechanism of polyploidy. To infer the evolution of PGI introns and PGI amino acid sequences, PGI cDNA and genomic sequences of other eukaryotes retrieved from GenBank and Ensembl were analyzed. The results of intron analyses did not support introns-early models because no ancient PGI intron was found. Parsimony analyses indicated that all PGI introns were inserted, and some introns were lost from different lineages of eukaryotes. The phylogenetic trees inferred from PGI amino acid sequences and genomic data were unable to reflect the authentic organismal phylogeny probably due to convergent evolution and lack of character. The utility of PGI intron sequences as a genetic marker was evaluated in three species of mullets. The results indicated that the PGI intorn sequences can be a potential marker in resolving interspecific phylogeny.
Chinese Abstract i
English Abstract iii
1. Introduction 1
2. Materials and methods 6
2.1 PGI genomic sequences in gray mullet 6
2.1.1 Specimen and DNA extraction 6
2.1.2 Amplification of PGI genomic sequences 6
2.1.3 Cloning and sequencing reaction 7
2.1.4 Determination of PGI genomic structures in gray mullet 8
2.2 Comparison of PGI amino acids and genomes in eukaryotes 8
2.2.1 PGI cDNA and genomic sequences in eukaryotes 8
2.2.2 Definition of intron position and phase 10
2.2.3 Comparison of PGI protein modules and intron positions 10
2.2.4 Phylogenetic analysis of PGI in eukaryotes 11
2.2.5 PGI intron loss and gain among different lineages 12
2.3 Utility of PGI intron sequences in reconstruction of mullet phylogeny 12
2.3.1 Specimens, EPIC-PCR, and sequencing 12
2.3.2 Phylogenetic analysis of gray mullet, largescale mullet, and greenback mullet 13
2.3.3 Neutrality tests 14
3. Results 15
3.1 PGI genomic structure in gray mullet 15
3.1.1 PGI-A genomic structure in gray mullet 15
3.1.2 PGI-B genomic structure in gray mullet 16
3.2 Evolution of PGI amino acid sequences and genomes in eukaryotes 17
3.2.1 Comparison of 60 PGI amino acid sequences 17
3.2.2 Characterizations of eukaryotic PGI genomes 19
3.2.3 Intron positions related to PGI secondary structural modules 21
3.2.4 PGI genomic evolution in eukaryotes 21
3.2.5 Phylogenetic relationships of PGI amino acid sequences in eukaryotes 22
3.2.6 Inference of PGI intron gains and losses in eukaryotes 23
3.3 Utility of PGI-B intron sequences as a genetic
marker 24
3.3.1 Genetic divergences 24
3.3.2 Neutrality tests 25
3.3.3 Phylogenetic analyses of largescale mullet, greenback mullet,and gray mullet 25
4. Discussion 27
5. References 31
Tables 36
Figures 53
Appendix 92
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