臺灣博碩士論文加值系統

高階植物的分子演化多以演化速率慢的胞器基因或核內低套數基因進行演化分析，演化速率較快的多套數基因，則少用以分析高階植物物種間的分類。本試驗利用14個物種的expansin基因進行物種間與物種內分子演化分析，分別探討多套數基因是否能做為高階植物的演化分類工具與expansin基因家族間的分子演化過程。演化分析試驗以演化早期的青綠藻做為標準，以胺基酸序列相似度篩選出直系同源基因，並以cDNA序列與胺基酸序列繪製最大似然法、最大概度法與近鄰結合法演化樹，探討物種間的高階演化關係，後又以物種內的expansin基因家族cDNA與胺基酸序列所繪製的演化樹探討物種內分子演化。試驗結果顯示若將直系同源基因的篩選標準提高，以核內多基因套數家族探討高階植物的演化分析便具有相當的可信度。在expansin基因的分子演化中，expansin基因的演化方向決定於基因重複與內隱子插入的事件，並從ExpA與ExpB兩次家族演化至ExpA、ExpB以及ExpL三次家族。以多套數基因進行演化分析，未來不只可進行高階植物的演化分類，還可了解植物間的分子演化過程，進一步連結演化過程中，多基因家族基因分子層面的改變如何影響植物的演化。

The phylogeny was the evolution of species and taxonomic grouping in an organism by using bioinformation. The ribosome DNA, chloroplast DNA and low-copy nuclear genes were used in phylogeny analysis, because their sequence divergences were slow. A new method that using multiple copies of nuclear genes could improve the robustness of phylogenic reconstruction. The expansin gene families were used in this study. There were three sub gene families in expansin gene which was partaking in plant development. The orthologous genes which show the highest similarity with the amino acid sequences of Ostreococcus tauri was selected from thirteen plant species. Then, the phylogeny tree was drawn by using Maximum likelihood (ML), Maximum parsimony (MP), Neighbor-joining (NJ) method with cDNA sequences and amino acid sequences. The expansin gene sequences were also compared the difference with molecular level in these species. The method was a useful tool to analyze the plant evolution at higher taxonomic levels and combined with molecular phylogeny of species by using multiple nuclear genes. However, the criterion of orthologous genes was stricted. At the molecular level, expansin gene was an ancestor gene in plant, and gene duplication and intron gain event happened in the course of plant evolution.

目錄
頁次
中文摘要 i
英文摘要 ii
目錄 iii
表目錄 v
圖目錄 vi
一、序言 1
二、前人研究 4
植物分子演化相關研究探討與演化樹的介紹 4
Expansin基因功能的研究 7
Expansin基因的分類與演化 11
三、材料與方法 15
刺角瓜 expansin基因來源 15
Expansin基因序列擷取與檔案整理 16
物種內直系同源基因篩選 16
物種間直系同源基因演化樹繪製與序列比對 17
物種內expansin 基因家族演化樹與序列分析 18
四、結果 19
Expansin基因序列擷取與檔案整理 19
物種內直系同源基因篩選 19
物種間直系同源基因演化樹繪製與序列比對 20
物種內expansin 基因家族演化樹與序列分析 22
五、討論 25
(一)、物種間expansin基因的演化 25
(二)、物種內expansin基因的演化 26
六、參考文獻 32

表目錄
頁次
Table 1. The expansin gene family in thirteen plant species 37
Table 2. The result of phylogenetic analysis 52

圖目錄
頁次
Fig. 1. Molecular phylogenetic anaylsis of expansin orthogous genes by cDNA sequences of thirteen plant species. 58
Fig. 2. Molecular phylogenetic anaylsis of expansin orthogous genes by amino acid sequences of thirteen plant species. 60
Fig. 3. The result of alignment fourteen expansin gene by using amino acid sequence. 61
Fig. 4. The illustration of the conserved motif in expansin orthogous proteins. 65
Fig. 5. The illustration of the conserved motif in expansin proteins of twelve species. 66

Albert, V. A. 2005. Parsimony, phylogeny, and genomics Oxford University Press, USA.
Albert, V. A., A. Backlund, K. Bremer, M. W. Chase, J. R. Manhart, B. D. Mishler, and K. C. Nixon. 1994. Functional constraints and rbcL evidence for land plant phylogeny. Ann. Mo. Bot. Gard. 81: 534-567.
Bailey, C. D. and J. J. Doyle. 1999. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Mol. Phylogenet. Evol. 13: 20-30.
Baxevanis, A. D. and A. D. O. Baxevanis. 2005. Bioinformatics: a practical guide to the analysis of genes and proteins 3rd ed, Wiley-Interscience.
Budzinski, I. G. F., T. B. Santos, T. Sera, D. Pot, L. G. E. Vieira, and L. F. P. Pereira. 2011. Expression patterns of three α-expansin isoforms in Coffea arabica during fruit development. Plant Biol. 13: 462-471.
Cai, Z., C. Penaflor, J.V. Kuehl, J. Leebens-Mack, J. E. Carlson, C. W. dePamphilis, J. L. Boore, and R. K. Jansen. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol. Biol. 6: 77.
Campbell N. A. and J. B. Reece. 2005. Biology 7th ed, International edition, San Fransisco.
Carpita, N.C. 1996. Structure and biogenesis of the cell walls of grasses. Annu. Rev. Plant Biol. 47: 445-476.
Chase, M. W., M. F. Fay, J. L. Reveal, D. E. Soltis, P. S. Soltis, A. A. Anderberg, M. J. Moore, R. G. Olmstead, P. J. Rudall. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161: 105-121.
Chase, M. W., D. E. Soltis, R. G. Olmstead, D. Morgan, D. H. Les, B. D. Mishler, M. R. Duvall, R. A. Price, H. G. Hills, and Y. L. Qiu. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann. Mo. Bot. Gard. 80: 528-580.
Cho, H. T. and H. Kende. 1997. Expansins in deepwater rice internodes. Plant Physiol. 113: 1137-1143.
Cosgrove, D. J. 2000. New genes and new biological roles for expansins. Curr. Opin. Plant Biol. 3: 73-78.
Cosgrove, D. J., P. Bedinger, and D. M. Durachko. 1997. Group I allergens of grass pollen as cell wall-loosening agents. Proc. Natl. Acad. Sci. U. S. A. 94: 6559.
Cosgrove, D. J., L. C. Li, H. T. Cho, S. Hoffmann-Benning, R. C. Moore, and D. Blecker. 2002. The growing world of expansins. Plant Cell Physiol. 43: 1436-1444.
Delsuc, F., H. Brinkmann, and H. Philippe. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6: 361-375.
Devos, K. M., J. K. M. Brown, and J. L. Bennetzen. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome research 12: 1075-1079.
Ding X., Y. Cao, L. Huang, J. Zhao, C. Xu, X. Li, and S. Wang. 2008. Activation of the indole-3-acetic acid–amido synthetase GH3-8 suppresses expansin expression and promotes salicylate-and jasmonate-independent basal immunity in rice. The Plant Cell Online 20: 228-240.
Fahlgren N., S. Jogdeo, K. D. Kasschau, C. M. Sullivan, E. J. Chapman, S. Laubinger, L. M. Smith, M. Dasenko, S. A. Givan, and D. Weigel. 2010. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. The Plant Cell Online 22: 1074-1089.
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
Fleming, A. J., S. McQueen-Mason, T. Mandel, and C. Kuhlemeier. 1997. Induction of leaf primordia by the cell wall protein expansin. Science 276: 1415-1418.
Friedman, N., M. Linial, I. Nachman, amd Pe''er D. 2000. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7: 601-620.
Georgelis, N., A. Tabuchi, N. Nikolaidis, and D. J. Cosgrove. 2011. Structure-function analysis of the bacterial expansin EXLX1. J. Biol. Chem. 286: 16814.
Girard, C., D. Rivard, A. Kiggundu, K. Kunert, S. C. Gleddie, C. Cloutier, and D. Michaud. 2007. A multicomponent, elicitor-inducible cystatin complex in tomato, Solanum lycopersicum. New Phytol. 173: 841-851.
The Angiosperm Phylogeny Group. 1998. An ordinal classification for the families of flowering plants. Ann. Mo. Bot. Gard. 85: 531-553.
The Angiosperm Phylogeny Group. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141: 399-436.
Harrison, C. J., and J. A. Langdale. 2006. A step by step guide to phylogeny reconstruction. Plant J. 45: 561-572.
Kardong, K.V. 2005. An introduction to biological evolution McGraw-Hill Higher Education.
Kende, H., K. Bradford, D. Brummell, H. T. Cho, D. Cosgrove, A. Fleming, C. Gehring, Y. Lee, S. McQueen-Mason, and J. Rose. 2004. Nomenclature for members of the expansin superfamily of genes and proteins. Plant Mol. Biol. 55: 311-314.
Kerff, F., A. Amoroso, R. Herman, E. Sauvage, S. Petrella, P. Filee, P. Charlier, B. Joris, A. Tabuchi, and N. Nikolaidis. 2008. Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization. Proc. Natl. Acad. Sci. U.S.A. 105: 16876.
Kim, J., H. T. Cho, and H. Kende. 2000. α-Expansins in the semiaquatic ferns Marsilea quadrifolia and Regnellidium diphyllum: evolutionary aspects and physiological role in rachis elongation. Planta 212: 85-92.
Lee, Y. and D. Choi. 2005. Biochemical properties and localization of the β-expansin OsEXPB3 in rice (Oryza sativa L.). Mol. Cells 20: 119-126.
Lee, Y., D. Choi, and H. Kende. 2001. Expansins: ever-expanding numbers and functions. Curr. Opin. Plant Biol. 4: 527-532.
Li, Y., C. P. Darley, V. Ongaro, A. Fleming, O. Schipper, S. L. Baldauf, S. J. McQueen-Mason. 2002. Plant expansins are a complex multigene family with an ancient evolutionary origin. Plant Physiol. 128: 854-864.
Lin, C., H. S. Choi, and H. T. Cho. 2011. Root hair-specific EXPANSIN A7 is required for root hair elongation in Arabidopsis. Mol. Cells 31: 393-397.
Lin, Y. T., C. W. Lin, C. H. Chung, J. C. Chen, H. H. Su, S. D. Yeh, F. J. Jan, and H. M. Ku. 2012. Differential gene expression in response to Papaya ringspot virus infection in Cucumis metuliferus using cDNA-amplified fragment length polymorphism analysis. (unpublished)

Ludidi, N., J. Heazlewood, C. Seoighe, H. Irving, and C. Gehring. 2002. Expansin-like molecules: novel functions derived from common domains. J. Mol. Evol. 54: 587-594.
Martinez-Castilla, L. P., and E. R. Alvarez-Buylla. 2003. Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny. Proc. Natl. Acad. Sci. U. S. A. 100: 13407.
Martin, T., M. Biruma, I. Fridborg, P. Okori, and C. Dixelius. 2011. A highly conserved NB-LRR encoding gene cluster effective against Setosphaeria turcica in sorghum. BMC Plant Biol. 11: 151-161.
Massa, A., H. Wanjugi, K. Deal, K. O''Brien, F. You, R. Maiti, A. Chan, Y. Gu, M. Luo, and O. Anderson. 2011. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes. Mol. Biol. Evol. 28: 2537-2547.
McQueen-Mason, S. and D. J. Cosgrove. 1994. Disruption of hydrogen bonding between plant cell wall polymers by proteins that induce wall extension. Proc. Natl. Acad. Sci. U. S. A. 91: 6574.
McQueen-Mason, S., S. C. Fry, D. M. Durachko, and D. J. Cosgrove. 1993. The relationship between xyloglucan endotransglycosylase and in-vitro cell wall extension in cucumber hypocotyls. Planta 190: 327-331.
Mourier, T. and D. C. Jeffares. 2003. Eukaryotic intron loss. Science 300: 1393-1393.
Nickrent, D. L., C. L. Parkinson, J. D. Palmer, and R. J. Duff. 2000. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol. Biol. Evol. 17: 1885-1895.
O''Kane, Jr S. L. and I. A. Al-Shehbaz. 2003. Phylogenetic position and generic limits of Arabidopsis (Brassicaceae) based on sequences of nuclear ribosomal DNA. Ann. Mo. Bot. Gard. 90: 603-612.
Olsen K. M. and B. A. Schaal. 1999. Evidence on the origin of cassava: phylogeography of Manihot esculenta. Proc. Natl. Acad. Sci. U. S. A. 96: 5586.
Olsen K. M. and M. D. Purugganan. 2002. Molecular evidence on the origin and evolution of glutinous rice. Genetics 162: 941-950.
Paterson A. H. 2006. Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nat. Rev. Genet. 7: 174-184.
Qiu Y. L., J. Lee, F. Bernasconi-Quadroni, D. E. Soltis, P. S. Soltis, M. Zanis, E. A. Zimmer, Z. Chen,V. Savolainen, and M. W. Chase. 1999. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402: 404-407.
Rose J. K. C., H. H. Lee, and A. B. Bennett. 1997. Expression of a divergent expansin gene is fruit-specific and ripening-regulated. Proc. Natl. Acad. Sci. U. S. A. 94: 5955.
Roy S. W. and M. Irimia. 2009. Mystery of intron gain: new data and new models. Trends Genet. 25: 67-73.
Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
Sang, T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Mol. Biol. 37: 121-147.
Shcherban T. Y., J. Shi, D. M. Durachko, M. J. Guiltinan, S. J. McQueen-Mason, M. Shieh, and D.J. Cosgrove. 1995. Molecular cloning and sequence analysis of expansins-a highly conserved, multigene family of proteins that mediate cell wall extension in plants. Proc. Natl. Acad. Sci. U. S. A. 92: 9245.
Tamura K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739.
Tarrio R., F. J. Ayala, and F. Rodriguez-Trelles. 2008. Alternative splicing: a missing piece in the puzzle of intron gain. Proc. Natl. Acad. Sci. U. S. A. 105: 7223.
Vannerum K., M. J. J. Huysman, R. De Rycke, M. Vuylsteke, F. Leliaert, J. Pollier, U. Lutz-Meindl, J. Gillard, L. De Veylder, and A. Goossens. 2011. Transcriptional analysis of cell growth and morphogenesis in the unicellular green alga Micrasterias (Streptophyta), with emphasis on the role of expansin. BMC Plant Biol. 11: 128.