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研究生: 林佳賢
Jia-Sian Lin
論文名稱: 利用粒腺體全基因體DNA 序列瞭解 台灣小雨蛙與近親種的演化及親源關係
Evolution and phylogeny of Microhyla fissipes and its relavent taxa infering from mitogenome
指導教授: 劉阜果
Fu-Guo Robert Liu
口試委員:
學位類別: 碩士
Master
系所名稱: 生醫理工學院 - 生命科學系
Department of Life Science
論文出版年: 2018
畢業學年度: 106
語文別: 中文
論文頁數: 107
中文關鍵詞: 小雨蛙親緣性粒腺體基因組序列
外文關鍵詞: Microhyla fissipes
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  • 小雨蛙 (Microhyla fissipes)在台灣台南(模式地點) 首次被發表命名,但並沒有被廣泛接受。 本研究,作者使用從宜蘭收集的樣本代表台灣樣本,並完成完整的線粒體基因組序列(登錄號:MF673131),用以研究Microhyla fissipes 與其近親的親緣關係,特別是希望瞭解與中國樣本(NC_009422)的差異。儘管我們的樣本(16,729個鹼基對)的基因與及基因順序其他兩棲動物幾乎相同,但台灣和中國的樣本之間序列上已有了一些差異。 有趣的是,我們發現ND5 和ND6 基因與其他基因演化非常不同。另外,對基因中所使用的密碼子,進行三個位元的統計分析發現,第二個位元使用胸腺嘧啶的比例較高,在第三個位元使用使用鳥嘌呤的比例明顯較低。


    Microhyla fissipes was first recognized in Tainan, Taiwan (type locality), however it is not highly accepted. Herein, author used the sample from Yi-Lan, Taiwan as a representative of Taiwan samples and obtained the complete mitochondrial genome sequence (accession
    number: MF673131) in order to study the phylogeny of Microhyla fissipes and its relevants, especially in the comparison with the China sample (NC_009422). Although the genome of our sample (16,729 base pairs) contains genes and gene order almost identical to other amphibians’, some variations have been accumulated between Taiwan and China samples. Interestingly, we noticed that ND5 and ND6 genes evolved very differently from other genes. Also there were strongly codon usage bias with high thymine frequency at the second codon and very low guanine frequency at the third codon.

    中文摘要 .................................................................................................................................. ii Abstract ........................................................................................................................................... iii 誌謝 ........................................................................................................................................... iv 目錄 .......................................................................................................................................... v 表目錄.................................................................................................................................................. vii 圖目錄.............................................................................................................................................. .. viii 縮寫檢索表.........................................................................................................................................ix 1. 緒論 .............................................................................................................................................1 1.1 小雨蛙 .....................................................................................................................................1 1.2 粒腺體.......................................................................................................................................1 1.3 關於粒腺基因體遺傳疾病.....................................................................................................3 1.4 分子生物技術的應用...............................................................................................................3 1.5 過去利用粒腺基因體對姬蛙屬(Microhyla)與狹口蛙屬(Kaloula)的研究.............................4 1.6 研究內容..................................................................................................................................5 2. 材料與方法 ...................................................................................................................................6 2.1 樣品 .........................................................................................................................................6 2.2 粗萃 .........................................................................................................................................6 2.3 引子 (primer) 設計................................................................................................................6 2.4 聚合酶連鎖反應(PCR)...........................................................................................................6 2.5 純化 .........................................................................................................................................7 2.6 定序 ...........................................................................................................................................7 2.7 整合序列資料...........................................................................................................................7 2.8 分析基因序列...........................................................................................................................7 3. 結果 ...............................................................................................................................................9 3.1 粒腺體基因...............................................................................................................................9 3.2 姬蛙屬 (Microhyla) 與狹口蛙屬(Kaloula) 基因差異.........................................................9 3.3 演化樹分析.............................................................................................................................10 3.4 密碼子現象.............................................................................................................................10 3.5 D-LOOP 與L 鏈複製起點...................................................................................................11 4. 討論 .............................................................................................................................................12 4.1 ND5 與 ND6 演化速率較特殊..........................................................................................12 4.2 台灣與中國M. fissipes 為相同物種......................................................................................12 5. 參考文獻 .....................................................................................................................................14

    Atsushi K., et al. (2005). "Molecular Phylogeny of the Ranid Frogs from Southwest
    India Based on the Mitochondrial Ribosomal RNA Gene Sequences. " Zoological
    Science. 22(5):525-534
    Anderson, S., et al., Sequence and organization of the human mitochondrial genome.
    Nature, 1981. 290(5806): p. 457-65.
    Alberts B, J.A., Lewis J, et al., Electron-Transport Chains and Their Proton Pumps.
    Molecular Biology of the Cell, New York: Garland Science; 2002. 4th edition.
    Alston, C.L., et al., The genetics and pathology of mitochondrial disease. J Pathol,
    2017. 241(2): p. 236-250.
    Boulenger, G. A. (1884). "Descriptions of new species of reptiles and batrachians in
    the British Museum. "—Part. II. Ann. Mag. Nat. Hist., Series 5(13): 396–398.
    Baertling, F., et al., A guide to diagnosis and treatment of Leigh syndrome. J Neurol
    Neurosurg Psychiatry, 2014. 85(3): p. 257-65.
    Balint, B. and K.P. Bhatia, Dystonia: an update on phenomenology, classification,
    pathogenesis and treatment. Curr Opin Neurol, 2014. 27(4): p. 468-76.
    Beale, G., The discovery of mustard gas mutagenesis by Auerbach and Robson in
    1941. Genetics, 1993. 134(2): p. 393-9.
    Chang, D.D. and D.A. Clayton, Priming of human mitochondrial DNA replication
    occurs at the light-strand promoter. Proc Natl Acad Sci U S A, 1985. 82(2): p. 351-5.
    Carelli, V., et al., Biochemical features of mtDNA 14484 (ND6/M64V) point mutation
    associated with Leber's hereditary optic neuropathy. Ann Neurol, 1999. 45(3): p. 320-8.
    Darriba D., T. G. L., Doallo R., Posada D. (2012). "jModelTest 2: more models, new
    heuristics and parallel computing." Nature Methods.
    Davidzon, S. D. G. (2005). "Mitochondrial DNA and disease"." Department of
    Neurology, Columbia University Medical Center.
    Duméril, A. H. a. G. B. (1841). "Erpetologie generale ou Histoire Naturelle complete
    des reptiles." Paris 8.
    Doda, J.N., C.T. Wright, and D.A. Clayton, Elongation of displacement-loop strands
    in human and mouse mitochondrial DNA is arrested near specific template sequences.
    Proc Natl Acad Sci U S A, 1981. 78(10): p. 6116-20.
    Esposito, D., L.A. Garvey, and C.S. Chakiath, Gateway cloning for protein
    expression. Methods Mol Biol, 2009. 498: p. 31-54.
    Fish, J., N. Raule, and G. Attardi, Discovery of a major D-loop replication origin
    reveals two modes of human mtDNA synthesis. Science, 2004. 306(5704): p. 2098-101.
    Giege, R, et al. (1998) Universal rules and idiosyncratic features in tRNA identity.
    Nucleic Acids Res 26: 5017-5035
    Guindon S., D. J. F., Lefort V., Anisimova M., Hordijk W., Gascuel O. (2003). " A
    simple, fast, and accurate algorithm to estimate large phylogenies by maximum
    likelihood." Syst. Biol 59: 307–321.
    Grada, A. and K. Weinbrecht, Next-generation sequencing: methodology and
    application. J Invest Dermatol, 2013. 133(8): p. e11.
    Hasan, M., et al. (2012). "Cryptic Anuran Biodiversity in Bangladesh Revealed by
    Mitochondrial 16S rRNA Gene Sequences." Zootaxa 29: 162–172.
    Hendrix ; Gawor, A. V., Miguel ; Ziegler, Thomas (2008). "The tadpole of the
    Narrow-mouthed Frog Microhyla fissipes from Vietnam." ZOOTAXA.(1675): 67-68.
    Hoi-SenYong, S.-L. S., Wayan Suanac, Praphathip Eamsobhanad, Phaik-Eem Lim
    (December 2016). "Complete mitochondrial genome of Orthetrum dragonflies and
    molecular phylogeny of Odonata." Biochemical Systematics and Ecology 69: 124-131.
    Huelsenbeck J.P., R. F. R. (2001). "MrBayes: Bayesian Inference of Phylogenetic
    Trees." Bioinformatics 17: 754-755. Holt, I.J., H.E. Lorimer, and H.T. Jacobs, Coupled
    leading- and lagging-strand synthesis of mammalian mitochondrial DNA. Cell, 2000.
    100(5): p. 515-24.
    Igawa, T., et al. (2008). "Complete mitochondrial genomes of three neobatrachian
    anurans: a case study of divergence time estimation using different data and calibration
    settings." Gene 407(1-2): 116-129.
    Jaryal, A.K., Nobel Prize in Physiology or Medicine for the year 2007. Indian J
    Physiol Pharmacol, 2007. 51(4): p. 423-4.
    Kuramoto, M. S. H. J. (2006). "Morphological and acoustic comparisons of
    Microhyla ornata, M. fissipes, and M. okinavensis (Anura: Microhylidae). ." Current
    Herpetology 25: 15-27.
    Kervinen, M., et al., The MELAS mutations 3946 and 3949 perturb the critical
    structure in a conserved loop of the ND1 subunit of mitochondrial complex I. Hum Mol
    Genet, 2006. 15(17): p. 2543-52.
    L., S. D. (1998). "PAUP*: Phylogenetic analysis using parsimony (and other
    methods), version 4.0."
    Lin, L. Y., et al. (1991). "Maternal transmission of mitochondrial DNA in ducks."
    Biochem Biophys Res Commun 168(1): 188-193.
    Larizza, A., et al., Lineage specificity of the evolutionary dynamics of the mtDNA
    D-loop region in rodents. J Mol Evol, 2002. 54(2): p. 145-55.
    Matsui M, I. H.,et al. (2005). "Taxonomic relationships within the pan-oriental
    narrow-mouth toad Microhyla ornata as revealed by mtDNA analysis (Amphibia, Anura,
    Microhylidae)." Zoolog Sci. 22(6): 711.
    Marzuki, S., et al., Normal variants of human mitochondrial DNA and translation
    products: the building of a reference data base. Hum Genet, 1991. 88(2): p. 139-45.
    Mindell, D.P., M.D. Sorenson, and D.E. Dimcheff, An extra nucleotide is not
    translated in mitochondrial ND3 of some birds and turtles. Molecular Biology and
    Evolution, 1998. 15(11): p. 1568-1571.
    Mitchell, A.L., et al., Sequence variation in mitochondrial complex I genes: mutation
    or polymorphism? J Med Genet, 2006. 43(2): p. 175-9.
    Michel, B. and H.R. Bosshard, Spectroscopic analysis of the interaction between
    cytochrome c and cytochrome c oxidase. J Biol Chem, 1984. 259(16): p. 10085-91.
    Ojala, D., J. Montoya, and G. Attardi, tRNA punctuation model of RNA processing in
    human mitochondria. Nature, 1981. 290(5806): p. 470-4.
    Papetti, C., et al. (2007). "Antarctic fish mitochondrial genomes lack ND6 gene." J
    Mol Evol 65(5): 519-528.
    Patterson, J., Chamberlain, B., Thayer, D. 2006. Finch TV Version 1.4.0. Retrieved
    from http://www.geospiza.com/Products/finchtv.shtml
    Plescia, O.J., et al., Production of antibodies to soluble RNA (sRNA). Proc Natl Acad Sci
    U S A, 1965. 54(4): p. 1281-5
    Pecina, P., et al., Genetic defects of cytochrome c oxidase assembly. Physiol Res, 2004.
    53 Suppl 1: p. S213-23.
    Raeymaekers, L., General principles of quantitative PCR. Methods Mol Med, 1999.
    26: p. 31-41.
    Schimmel P (1987) Aminoacyl tRNA synthetases: general scheme of
    structure-function relationships in the polypeptides and recognition of transfer RNAs.
    Annu Rev Biochem 56: 125-158
    Stejneger (1901). "Diagnoses of Eight New Batrachians and Reptiles from the Riu
    Kiu Archipelago, Japan." Proceedings of the Biological Society of Washington 14:
    189-191.
    Siebert, P.D., Quantitative rt-PCR. Methods Mol Med, 1999. 26: p. 61-85.
    Tsukihara, T., et al., The whole structure of the 13-subunit oxidized cytochrome c
    oxidase at 2.8 A. Science, 1996. 272(5265): p. 1136-44.
    Xuan, J., et al., Next-generation sequencing in the clinic: promises and challenges.
    Cancer Lett, 2013. 340(2): p. 284-95.
    Yang, Y. J., et al. (1994). "Variation in mitochondrial DNA and population structure
    of the Taipei treefrog Rhacophorus taipeianus in Taiwan." Mol Ecol 3(3): 219-228.
    Zhang, P., et al. (2005). "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.
    呂光洋 (1980). "台灣產兩棲類隻棲息環境簡介." 科學教育雙月刊 3(8): 47-50.
    呂光洋、陳世煌 (1986). "台灣的兩棲類動物." 台灣省政府教育廳.
    陳嘉芬 (2002)―現代遺傳學Ⅱ",藝軒。
    楊懿如 (1998)"賞蛙圖鑑-台灣蛙類野外觀察指南",中華名國自然與生態攝影學會
    出版,143.

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