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dc.contributor.advisorHsiao-Wei Kaoen_US
dc.contributor.authorLin, Chu-Yinen_US
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The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians. Gene. 346:133-143.zh_TW
dc.description.abstract裘氏鱷頭冰魚(Champsocephalus gunnari)是南極冰魚的其中一員。Papetti等人(2007)曾提出一個假說:所有的南極冰魚都不具有ND6與tRNAGlu基因,並且南極冰魚的共同祖先可能已失去這二個基因。為了測試這個假說,本研究藉由PCR、選殖(cloning)以及定序(sequencing)得到裘氏鱷頭冰魚的完整粒線體DNA序列,發現裘氏鱷頭冰魚具有ND6與tRNAGlu,此與Papetti等人的假說不符。和一般脊椎動物動物不同的是,裘氏鱷頭冰魚的ND6與tRNAGlu轉位(transpose)到tRNAThr及tRNAPro之間,而不是位在ND5與cyt b之間。此外,從ND6到控制區(control region,簡稱CR)的DNA片段串聯重複(tandem duplication)了一次,使其粒線體基因體結構與目前已知的脊椎動物都不同。我們還發現在不同個體中,第一個重複片段裡的基因組成有差異。第一型的個體擁有完整的ND6及tRNAGlu,第二型有半個ND6但是沒有tRNAGlu,第三型則沒有ND6也沒有tRNAGlu。我們推測串聯重複後再隨機失去模式(tandem duplication-random loss model,簡稱TDRL model) (Moritz and Brown 1986; Moritz and Brown 1987)是形成裘氏鱷頭冰魚粒線體基因新的排列順序的主要機制。冰魚的親緣關係樹並不支持ND6及tRNAGlu在南極冰魚的共同祖先就已失去了的假說,除非裘氏鱷頭冰魚後來又重新得到ND6及tRNAGlu。另一個可能的假說是南極冰魚各支系分別失去ND6和tRNAGlu,而裘氏鱷頭冰魚是其中沒有失去ND6和tRNAGlu的一個支系。zh_TW
dc.description.abstractIt has been proposed that loss of ND6 and tRNAGlu is shared by all Antarctic notothenioid fishes, and likely occurs in their common ancestor (Papetti et al. 2007). To test this hypothesis, the complete mitochondrial (mt) DNA sequences of mackerel icefish (Champsocephalus gunnari), a member of Antarctic notothenioids, were obtained by polymerase chain reactions (PCR), cloning, and sequencing. In contrast to the proposal of Papetti et al. (2007), ND6 and tRNAGlu are present in the mt genome of mackerel icefish. Notably, ND6 and tRNAGlu are transposed to the position between tRNAThr and tRNAPro compared to the position between ND5 and cyt b in the ordinary vertebrate mt genomes. In addition, the segment from ND6 to control region (CR) tandemly duplicates once. Variations in gene content of the first duplicate were observed among different individuals. The variations include a full-length ND6 and tRNAGlu (referred as type-1), a truncated ND6 and loss of tRNAGlu (referred as type-2), and loss of both ND6 and tRNAGlu (referred as type-3). We proposed that tandem duplication-random loss model (TDRL model) (Moritz and Brown 1986; Moritz and Brown 1987) may account for the novel mt genome of mackerel icefish. Phylogenetic tree of notothenioids does not support that the loss of ND6 and tRNAGlu occurred at the common ancestor of Antarctic notothenioids unless ND6 and tRNAGlu were regained in mackerel icefish. The alternative hypothesis was that ND6 and tRNAGlu were lost independently in the different lineages of nototheniods and mackerel icefish was one of the lineages that retained ND6 and tRNAGlu.en_US
dc.description.tableofcontentsChinese abstract i English abstract ii Contents iii List of tables v List of figures vi List of supplementary tables vii 1.Introduction 1 2. Meterials and methods 4 2.1. Specimens and DNA Extraction 4 2.2 Amplification of Mitochondrial Genome by Polymerase Chain Reaction 4 2.3 Cloning and Plasmid Extraction 6 2.4 Sequencing Reaction 6 2.5 Gene Identification and Genome Analysis 7 2.6 Test of ND6 and tRNAGlu Transposition 7 2.7 The Pairwise Rate Ratios between Nonsynonymous Substitutions per Site (dN) and Synonymous Substitutions per Site (dS) of ND6, ATP6, ATP8, and cyt b 8 2.8 Phylogenetic Analyses 9 3. Results 12 3.1 Mt Geonome of C. gunnari 12 3.2 Ribosomal RNA and Transfer RNA Genes 12 3.3 Protein-coding Genes 13 3.4 Non-coding Region 13 3.5 Variations in Gene Content of the First Copy of the Duplicate 15 3.6 Synonnymous versus Nonsynonymous Substitutions of ND6, ATP6, ATP8, and cyt b 17 3.7 Phylogenetic Analysis 17 4. Discussion 19 4.1 The Presence of ND6 in Mt Genome of Mackerel Icefish 19 4.2 A Novel Organization of Mackerel Icefish Mt Genome 19 4.3 Retention of ND6 and CR Duplicates 20 4.4 Possible Mechanisms for Gene Duplication and Trasposition 21 4.5 Phylogenetic Implications 23 5. Reference 25 Tables 32 Figures 37 Supplementary tables 44en_US
dc.subjectgene duplicationen_US
dc.subjectgene transpositionen_US
dc.titleComplete Mitochondrial Genome of Mackerel Icefish (Champsocephalus gunnari): Retention of ND6 and tRNAGlu, and a Novel Genome Organizationen_US
dc.typeThesis and Dissertationzh_TW
item.openairetypeThesis and Dissertation-
item.fulltextno fulltext-
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