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研究生: 何紹瑋
Ho, Shao-Wei
論文名稱: 石櫟屬物種生理生態性狀親緣訊息與蠟生合成基因正向天擇
Phylogenetic signal in eco-physiological traits and signature of positive selection in biosynthetic genes in stone oaks (Lithocarpus, Fagaceae)
指導教授: 廖培鈞
Liao, Pei-Chun
學位類別: 博士
Doctor
系所名稱: 生命科學系
Department of Life Science
論文出版年: 2016
畢業學年度: 104
語文別: 中文
論文頁數: 89
中文關鍵詞: 功能性基因演化親緣訊息生理生態
英文關鍵詞: functional gene evolution, phylogenetic signal, eco-physiological
DOI URL: https://doi.org/10.6345/NTNU202203871
論文種類: 學術論文
相關次數: 點閱:120下載:5
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  • 有些植物表皮細胞中的蠟生合成基因生合成蠟後,經通道蛋白運輸至細胞外堆疊,形成物理性屏障的結晶狀(epicuticular wax crystal)構造,常被認為與化學性防禦特徵(如:酚酸)之間有權衡關係。此外,葉表蠟有無的適應也可能反映在蠟生合成基因及受蠟影響的生態特徵上,如光合作用效率。本研究以石櫟屬物種作為材料,利用遺傳及生理生態分析探討葉表蠟結晶的有/無特徵是否為適應的結果。首先使用6個參考基因重建石櫟屬的親緣關係,發現距今約1400萬年前至800萬年前,至少出現3次獨立由無蠟到產生蠟結晶的特徵轉換的演化事件。在蠟骨架生合成(CER1、CER3)、調節性(CER7)、及運輸蛋白(CER5)等基因中,僅發現CER1在由無蠟到產生蠟結晶的特徵轉換時有正向天擇訊號;生理生態檢測中,蠟結晶均與酚酸及光合作用指數無顯著相關。但Y(II)及δ15N等光合作用指數在CER1基因樹呈現顯著的親緣訊息,顯示光合作用效率在種間的差異反應在蠟骨架合成的演化上。本研究推論,石櫟屬物種在中新世中期至上新世初期發生特徵轉換,當時劇烈的氣候變化也反映了蠟結晶生合成基因的正向天擇及光合作用效率上。

    The epicuticular waxes are synthesized and transported by wax-related genes in plants. The wax crystals serve as defensive traits and are considered as a trade-off between physical and chemical traits e.g. phenolic acids. Besides, the leaf epicuticular wax may be related to photosynthetic efficiency. I select stone oaks (Lithocarpus, Fagaceae) as our research materials and obtain genetic and physiological data to investigate whether the presence/absences of leaf epicuticular wax is an adaptive trait in stone oaks. The phylogenetic relationship of stone oaks reconstructed by six reference genes showed that trait shifts at least three times from non-crystalized waxy into crystalized waxy epidermis since 140 Mya to 80Mya. I sequenced and tested positive selection signals in four wax-related genes, CER1, CER3, CER5, and CER7, which are categorized as two, backbone synthetic genes, one regulatory, and one transporter genes, respectively. Signature of positive selection on CER1 at three trait transitional events of non-crystalized wax to crystalized wax imply the adaptive feature of presence of leaf epicutucular wax in Lithocarpus. The eco-physiologic analysis showed that contents of phenolic acids and photosynthetic indices are not correlated with leaf epicuticular wax, but certain photosynthetic indices, Y(II), and δ15N showed significant phylogenetic signals associated with the CER1 gene tree. These results suggest the intraspecific differences of photosynthetic efficiency are response to the evolution of backbone gene. In conclusion, the trait shift events of leaf epicuticular wax in stone oaks that are inferred during the period of dramatic climate change during the Middle Miocene to Early Pliocene may be related to the positive selection of wax synthetic genes and associated with difference of photosynthetic efficiency between species.

    中文摘要 2 英文摘要 3 前言 4 研究材料與方法 16 結果 29 討論 41 結論 51 參考文獻 53 圖示 61 表格 68 附錄 87

    Abouheif E. 1999. A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research 1(8): 895-909.
    Agrawal AA. 2007. Macroevolution of plant defense strategies. Trends in Ecology & Evolution 22(2): 103-109.
    Anisimova M, Nielsen R, Yang ZH. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164(3): 1229-1236.
    Barthlott W, Neinhuis C, Cutler D, Ditsch F, Meusel I, Theisen I, Wilhelmi H. 1998. Classification and terminology of plant epicuticular waxes. Botanical Journal of the Linnean Society 126(3): 237-260.
    Bernard A, Domergue F, Pascal S, Jetter R, Renne C, Faure JD, Haslam RP, Napier JA, Lessire R, Joubes J. 2012. Reconstitution of plant alkane biosynthesis in yeast demonstrates that Arabidopsis ECERIFERUM1 and ECERIFERUM3 are core components of a very-long-chain alkane synthesis complex. Plant Cell 24(7): 3106-3118.
    Bernard A, Joubes J. 2013. Arabidopsis cuticular waxes: Advances in synthesis, export and regulation. Progress in Lipid Research 52(1): 110-129.
    Blomberg SP, Garland T, Ives AR. 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57(4): 717-745.
    Blum A. 2009. Effective use of water (EUW) and not water-use efficiency (WUE) is the target of crop yield improvement under drought stress. Field Crops Research 112(2-3): 119-123.
    Bourdenx B, Bernard A, Domergue F, Pascal S, Leger A, Roby D, Pervent M, Vile D, Haslam RP, Napier JA, et al. 2011. Overexpression of Arabidopsis ECERIFERUM1 promotes wax very-long-chain alkane biosynthesis and influences plant response to biotic and abiotic stresses. Plant Physiology 156(1): 29-45.
    Branden CI. 1999. Introduction to protein structure: Garland Science.
    Campbell SA, Kessler A. 2013. Plant mating system transitions drive the macroevolution of defense strategies. Proceedings of the National Academy of Sciences of the United States of America 110(10): 3973-3978.
    Cheeke PR. 1989. Toxicants of plant origin: Alkaloids. Boca Raton, Florida: CRC Press.
    Chou PY, Fasman GD. 1974. Conformational Parameters for Amino-Acids in Helical, Beta-Sheet, and Random Coil Regions Calculated from Proteins. Biochemistry 13(2): 211-222.
    Delport W, Poon AFY, Frost SDW, Pond SLK. 2010. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26(19): 2455-2457.
    Deng M, Li QS, Yang ST, Liu YC, Xu J. 2013. Comparative morphology of leaf epidermis in the genus Lithocarpus and its implication in leaf epidermal feature evolution in Fagaceae. Plant Systematics and Evolution 299(3): 659-681.
    Dodd RS, Afzal-Rafii Z. 2000. Habitat-related adaptive properties of plant cuticular lipids. Evolution 54(4): 1438-1444.
    Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
    Dray S, Dufour AB. 2007. The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software 22(4): 1-20.
    Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29(8): 1969-1973.
    Engel DE, DeGrado WF. 2004. Amino acid propensities are position-dependent throughout the length of alpha-helices. Journal of Molecular Biology 337(5): 1195-1205.
    Engelberth J. 2006. Plant Physiology. Sunderland, UK: Sinauer Associates.
    Farquhar GD, Ehleringer JR, Hubick KT. 1989. Carbon isotope discrimination and photosynthesis. Annual Review of Plant Physiology and Plant Molecular Biology 40: 503-537.
    Fordyce JA, Agrawal AA. 2001. The role of plant trichomes and caterpillar group size on growth and defence of the pipevine swallowtail Battus philenor. Journal of Animal Ecology 70(6): 997-1005.
    Fourquin C, Vinauger-Douard M, Fogliani B, Dumas C, Scutt CP. 2005. Evidence that CRABS CLAW and TOUSLED have conserved their roles in carpel development since the ancestor of the extant angiosperms. Proceedings of the National Academy of Sciences of the United States of America 102(12): 4649-4654.
    Fraenkel GS. 1959. The Raison d'Être of Secondary Plant Substances: These odd chemicals arose as a means of protecting plants from insects and now guide insects to food. Science 129(3361): 1466-1470.
    Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science 296(5568): 750-752.
    Fu WJ, Chi Z, Ma ZC, Zhou HX, Liu GL, Lee CF, Chi ZM. 2015. Hydrocarbons, the advanced biofuels produced by different organisms, the evidence that alkanes in petroleum can be renewable. Applied Microbiology and Biotechnology 99(18): 7481-7494.
    Furstenberg-Hagg J, Zagrobelny M, Bak S. 2013. Plant defense against insect herbivores. International Journal of Molecular Sciences 14(5): 10242-10297.
    Gambino G, Perrone I, Gribaudo I. 2008. A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochemical Analysis 19(6): 520-525.
    Giese BN. 1975. Effects of light and temperature on the composition of epicuticular wax of barley leaves. Phytochemistry 14(4): 921-929.
    Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59(3): 307-321.
    Hackathon R, Bolker B, Butler M, Cowan P, Vienne D, Eddelbuettel D 2011. Phylobase: Base package for phylogenetic structures and comparative data, R package version 0.6. 3.
    Hall R. 2002. Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions, model and animations. Journal of Asian Earth Sciences 20(4): 353-431.
    Hall TA 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series. 95-98.
    Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24(1): 129-131.
    Haworth M, McElwain J. 2008. Hot, dry, wet, cold or toxic? Revisiting the ecological significance of leaf and cuticular micromorphology. Palaeogeography Palaeoclimatology Palaeoecology 262(1-2): 79-90.
    Heled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27(3): 570-580.
    Hill RS. 1998. Fossil evidence for the onset of xeromorphy and scleromorphy in Australian Proteaceae. Australian Systematic Botany 11(3-4): 391-400.
    Ho CS. 1986. A Synthesis of the Geologic Evolution of Taiwan. Tectonophysics 125(1-3): 1-16.
    Hoffmann A. 2014. Evolutionary limits and constraints. The Princeton guide to evolution. Princeton University Press, Princeton: 247-252.
    Holmes MG, Keiller DR. 2002. Effects of pubescence and waxes on the reflectance of leaves in the ultraviolet and photosynthetic wavebands: a comparison of a range of species. Plant Cell and Environment 25(1): 85-93.
    Hooker TS, Lam P, Zheng HQ, Kunst L. 2007. A core subunit of the RNA-processing/degrading exosome specifically influences cuticular wax biosynthesis in Arabidopsis. Plant Cell 19(3): 904-913.
    Huang C, Zhang Y, Bartholomew B 1999. Fagaceae. In: Wu Zhengyi PHRHD ed. Flora of China. Beijing, China: Science Press (Beijing) & Missouri Botanical Garden (St. Louis), 314-400.
    Jenks MA, Rich PJ, Ashworth EN. 1994. Involvement of cork cells in the secretion of epicuticular wax filaments on Sorghum bicolor (L) Moench. International Journal of Plant Sciences 155(5): 506-518.
    Jiang B, Guo T, Peng LW, Sun ZR. 1998. Folding type-specific secondary structure propensities of amino acids, derived from alpha-helical, beta-sheet, alpha/beta, and alpha+beta proteins of known structures. Biopolymers 45(1): 35-49.
    Jombart T, Balloux F, Dray S. 2010. adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics 26(15): 1907-1909.
    Kamilar JM, Cooper N. 2013. Phylogenetic signal in primate behaviour, ecology and life history. Philosophical Transactions of the Royal Society B-Biological Sciences 368(1618).
    Kannangara R, Branigan C, Liu Y, Penfield T, Rao V, Mouille G, Hofte H, Pauly M, Riechmann JL, Broun P. 2007. The transcription factor WIN1/SHN1 regulates cutin biosynthesis in Arabidopsis thaliana. Plant Cell 19(4): 1278-1294.
    Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26(11): 1463-1464.
    Kerstiens G. 2006. Water transport in plant cuticles: an update. Journal of Experimental Botany 57(11): 2493-2499.
    Koenig D, Jimenez-Gomez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, et al. 2013. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences of the United States of America 110(28): E2655-E2662.
    Kosma DK, Bourdenx B, Bernard A, Parsons EP, Lu S, Joubes J, Jenks MA. 2009. The Impact of Water Deficiency on Leaf Cuticle Lipids of Arabidopsis. Plant Physiology 151(4): 1918-1929.
    Kunst L, Samuels AL. 2003. Biosynthesis and secretion of plant cuticular wax. Progress in Lipid Research 42(1): 51-80.
    Lam P, Zhao LF, Eveleigh N, Yu Y, Chen XM, Kunst L. 2015. The exosome and trans-acting small interfering RNAs regulate cuticular wax biosynthesis during Arabidopsis inflorescence stem development. Plant Physiology 167(2): 323-U530.
    Lam P, Zhao LF, McFarlane HE, Aiga M, Lam V, Hooker TS, Kunst L. 2012. RDR1 and SGS3, Components of RNA-Mediated Gene Silencing, Are Required for the Regulation of Cuticular Wax Biosynthesis in Developing Inflorescence Stems of Arabidopsis. Plant Physiology 159(4): 1385-1395.
    Lee JY, Baum SF, Oh SH, Jiang CZ, Chen JC, Bowman JL. 2005. Recruitment of CRABS CLAW to promote nectary development within the eudicot clade. Development 132(22): 5021-5032.
    Lee SB, Suh MC. 2013. Recent Advances in Cuticular Wax Biosynthesis and Its Regulation in Arabidopsis. Molecular Plant 6(2): 246-249.
    Li NN, Xu CC, Li-Beisson YH, Philippar K. 2016. Fatty acid and lipid transport in plant cells. Trends in Plant Science 21(2): 145-158.
    Liao J-C. 1996. Fagaceae in flora of Taiwan. Editorial Committee of the Flora of Taiwan: Taipei 2: 51-123.
    Liu TK, Chen YG, Chen WS, Jiang SH. 2000. Rates of cooling and denudation of the Early Penglai Orogeny, Taiwan, as assessed by fission-track constraints. Tectonophysics 320(1): 69-82.
    Müller C. 2006. Biology of the plant cuticle. Blackwell Publishing Ltd: Oxford, UK.
    Manos PS, Cannon CH, Oh S-H. 2008. Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of western North America: recognition of a new genus, Notholithocarpus. Madrono 55(3): 181-190.
    Manos PS, Stanford AM. 2001. The historical biogeography of Fagaceae: Tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere. International Journal of Plant Sciences 162: S77-S93.
    Manos PS, Steele KP. 1997. Phylogenetic analyses of ''higher'' Hamamelididae based on plastid sequence data. American Journal of Botany 84(10): 1407-1419.
    Manos PS, Zhou ZK, Cannon CH. 2001. Systematics of Fagaceae: Phylogenetic tests of reproductive trait evolution. International Journal of Plant Sciences 162(6): 1361-1379.
    Matasci N, Hung LH, Yan ZX, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, et al. 2014. Data access for the 1,000 Plants (1KP) project. Gigascience 3.
    McFarlane HE, Shin JJH, Bird DA, Samuels AL. 2010. Arabidopsis ABCG transporters, which are required for export of diverse cuticular lipids, dimerize in different combinations. Plant Cell 22(9): 3066-3075.
    Moctezuma C, Hammerbacher A, Heil M, Gershenzon J, Mendez-Alonzo R, Oyama K. 2014. Specific polyphenols and tannins are associated with defense against insect herbivores in the tropical oak Quercus oleoides. Journal of Chemical Ecology 40(5): 458-467.
    Moles AT, Peco B, Wallis IR, Foley WJ, Poore AGB, Seabloom EW, Vesk PA, Bisigato AJ, Cella-Pizarro L, Clark CJ, et al. 2013. Correlations between physical and chemical defences in plants: tradeoffs, syndromes, or just many different ways to skin a herbivorous cat? New Phytologist 198(1): 252-263.
    Monneveux P, Belhassen E. 1996. The diversity of drought adaptation in the wide. Plant Growth Regulation 20(2): 85-92.
    Moran PA. 1950. Notes on continuous stochastic phenomena. Biometrika 37(1/2): 17-23.
    Mulroy TW. 1979. Spectral properties of heavily glaucous and non-glaucous leaves of a succulent rosette-plant. Oecologia 38(3): 349-357.
    Munkemuller T, Lavergne S, Bzeznik B, Dray S, Jombart T, Schiffers K, Thuiller W. 2012. How to measure and test phylogenetic signal. Methods in Ecology and Evolution 3(4): 743-756.
    Myers JHB, D. 1991. Phytochemical induction by herbivores. New York, NY, USA: John Wiley & Sons.
    Nielsen R, Yang ZH. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148(3): 929-936.
    Nixon KC, Crepet WL. 1989. Trigonobalanus (Fagaceae) - Taxonomic Status and Phylogenetic-Relationships. American Journal of Botany 76(6): 828-841.
    Ogburn RM, Edwards EJ. 2010. The ecological water-use strategies of succulent plants. Advances in Botanical Research 55: 179-225.
    Oh SH, Manos PS. 2008. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences. Taxon 57(2): 434-451.
    Paradis E, Claude J, Strimmer K. 2004. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20(2): 289-290.
    Perez-Harguindeguy N, Diaz S, Garnier E, Lavorel S, Poorter H, Jaureguiberry P, Bret-Harte MS, Cornwell WK, Craine JM, Gurvich DE, et al. 2013. New handbook for standardised measurement of plant functional traits worldwide. Australian Journal of Botany 61(3): 167-234.
    Pighin JA, Zheng HQ, Balakshin LJ, Goodman IP, Western TL, Jetter R, Kunst L, Samuels AL. 2004. Plant cuticular lipid export requires an ABC transporter. Science 306(5696): 702-704.
    Pond SLK, Frost SDW. 2005. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21(10): 2531-2533.
    Pond SLK, Frost SDW, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5): 676-679.
    Pond SLK, Posada D, Gravenor MB, Woelk CH, Frost SDW. 2006. GARD: a genetic algorithm for recombination detection. Bioinformatics 22(24): 3096-3098.
    R Core Team. 2013. R: A language and environment for statistical computing.
    Rambaut A. 2015. FigTree, ver. 1.4. 2. Available: http:/tree. bio. ed. ac. uk/software/figtree/Accessed on 28.
    Rambaut A, Suchard M, Xie D, Drummond A 2014. Tracer v1. 6.
    Rattan RS. 2010. Mechanism of action of insecticidal secondary metabolites of plant origin. Crop Protection 29(9): 913-920.
    Reina-Pinto JJ, Yephremov A. 2009. Surface lipids and plant defenses. Plant Physiology and Biochemistry 47(6): 540-549.
    Revell LJ. 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3(2): 217-223.
    Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539-542.
    Rosenthal GA, Berenbaum MR. 2012. Herbivores: Their interactions with secondary plant metabolites: Academic Press.
    Samuels L, Kunst L, Jetter R. 2008. Sealing plant surfaces: Cuticular wax formation by epidermal cells. Annual Review of Plant Biology 59: 683-707.
    Schaller AH, G.A. 2008. Induced plant resistance to herbivory. Berlin, Germany: Springer Science+Business Media.
    Shimodaira H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16(8): 1114-1116.
    Susilohadi S, Gaedicke C, Djajadihardja Y. 2009. Structures and sedimentary deposition in the Sunda Strait, Indonesia. Tectonophysics 467(1-4): 55-71.
    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution 30(12): 2725-2729.
    Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25(24): 4876-4882.
    Waters ER. 2003. Molecular adaptation and the origin of land plants. Molecular Phylogenetics and Evolution 29(3): 456-463.
    Williams RW, Chang A, Juretic D, Loughran S. 1987. Secondary Structure Predictions and Medium Range Interactions. Biochimica Et Biophysica Acta 916(2): 200-204.
    Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24(8): 1586-1591.
    Yeats TH, Rose JKC. 2013. The formation and function of plant cuticles. Plant Physiology 163(1): 5-20.
    Zhou W, Xia NH. 2012. Leaf epidermal features of Lithocarpus (Fagaceae) from China and their systematic significance. Botanical Journal of the Linnean Society 168(2): 216-228.

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