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研究生:黃朝慶
研究生(外文):Jao-ChingHuang
論文名稱:沼生水丁香基因體研究
論文名稱(外文):Genome sequence of Ludwigia palustris
指導教授:蔣鎮宇蔣鎮宇引用關係
指導教授(外文):Tzen-Yuh Chiang
學位類別:博士
校院名稱:國立成功大學
系所名稱:生命科學系碩博士班
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:2013
畢業學年度:101
語文別:中文
論文頁數:43
中文關鍵詞:沼生水丁香基因體定序基因註解親緣關係
外文關鍵詞:Ludwigia palustrisgenomesequencinggene annotationphylogeny
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沼生水丁香原產於北美洲,目前是台灣地區新歸化之柳葉菜科植物,本研究以次世代定序方式(Illumina, Solex)對此物種進行基因體分析。應用流式細胞儀測定得知其C-value為0.23pg,是現知水丁香屬C-value較少的,染色體數目為2n=16。推估沼生水丁香基因體大小為0.15 Gb,經定序片段組序與基因註解得到4,927條scaffolds,最長為676,406 bps,最短為5,004 bps,GC含量約占40.55%,Augustus軟體預測基因數為25,984個,最長基因為39,475 bps,最短為201 bps。 進一步為了解沼生水丁香與其他植物物種之基因體親緣關係,共選取Populus trichocarp, Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycine max 等5種雙子葉植物,並以水稻(Oryza sativa)為外群進行研究,同時自沼生水丁香基因體隨機選取142個同源基因,利用MEGA軟體探討物種親緣關係,所重建的基因樹中39個基因樹顯示沼生水丁香與P. trichocarp較為近緣,但基因樹狀圖中與其他物種關係卻呈現不同形式與比例。
Ludwigia palustris, native to North America, is newly naturalized Onagraceae plant in Taiwan. In this study, the next generation sequencing (Illumina, Solexa) was applied to analysis genomic sequences of L. palustris. The C-value of L. palustris (2n=16) using flow cytometry is 0.23pg, and is lower than other Ludwigia species. The Solexa technology is used for sequencing genome of L. palustris, and genome size is 0.15 Gb. After bioinformatics analyses, 4,927 scaffolds were assembled. The maximum length is 676,406 bps, the minimum length is 5,004 bps, and GC content is about 40.55%. Augustus program predicted 25,984 genes, the longest gene is 39,475 bps, and shortest gene is 201 bps. In this study, the genomes of other 5 dicotyledonous plants were selected, including Populus trichocarp, Arabidopsis thaliana, Cucumis sativus, Vitis vinifera and Glycine max, to reconstruct the phylogeny of these species with outgroup of Oryza sativa. The genealogical analysis of 142 randomly orthologous genes suggested that L. palustris and P. trichocarp were closely relative species for 39 orthologous genes, but these gene trees displayed different topologies with other species.
目錄
中文摘要 I
Abstract II
誌謝 III
目錄 IV
表目錄 VI
圖目錄 VII
附錄目錄 VIII
第壹章 緒言 1
一、基因體 ( Genome )研究 1
二、基因體大小之測定 6
三、基因體定序(sequencing)與註解(annonation) 7
四、沼生水丁香(Ludwigia palustris (L.) Elliott)介紹 8
五、研究目的 9
第貳章 材料與方法 10
一、研究材料 10
二、實驗方法 10
三、資料分析 12
第參章 結果 14
一、沼生水丁香C-value測定 14
二、沼生水丁香定序與註解 14
三、沼生水丁香親緣分析 15
第肆章 討論 17
一、沼生水丁香C-value與定序後基因體大小之比較 17
二、沼生水丁香親緣樹狀圖分析 18
第伍章 結論 19
第陸章 參考文獻 20
表 26
圖 31
附錄一:流式細胞儀實驗流程 42


表目錄
Table 1.Genome size of organism. 26
Table 2.Genome size and C-value of 6 plants. 26
Table 3. Materials for cytometry experiments and the C values estimated. 26
Table 4. C-values estimated of Ludwigia species.in Taiwan. 27
Table 5. Assembly and annotation statistics for the Ludwigia palustris. 27
Table 6. C-value and chromosome number of 6 species in the study. 28
Table 7.Tree pattern of Ludwigia palustris with Populus trichocarpa. 28
Table 8.Tree pattern of Ludwigia palustris with Cucumis sativus. 29
Table 9.Tree pattern of Ludwigia palustris with Arabidopsis thaliana. 29
Table 10.Tree pattern of Ludwigia palustris with Glycine max. 30
Table 11.Tree pattern of Ludwigia palustris with Vitis vinifera. 30

圖目錄
Fig 1.Habit(A) and fruit(B) of Ludwigia palustris. 31
Fig 2.Phylogeny of angiosperm. (Copy from Angiosperm Phylogeny Website. Version 12, July 2012. http://www.mobot.org/MOBOT/research/APweb/.) 32
Fig 3.Phylogeny of 6 plants in the study. 33
Fig 4. Gene tree of model{[(Lp,Pt),At],[Cs,(Gm,Vv)]},Os 34
Fig 5. Gene tree of model {[(Lp,Pt),At],[Vv,(Cs,Gm)]},Os 34
Fig 6. Gene tree of model {[(Lp,Pt),At],[Gm,(Cs,Vv)]},Os 34
Fig 7. Gene tree of model {[(Lp,Pt),Cs],Gm},At,},Vv},Os 35
Fig 8. Gene tree of model {{[(Lp,Pt),At],Vv},(Cs,Gm)},Os 35
Fig 9. Gene tree of model {{[(Cs,Vv),Gm],At}(Lp,Pt)}, Os 35
Fig 10. Gene tree of model {{[(Gm,Vv),Cs],At},(Lp,Pt)},Os 36
Fig 11. Gene tree of model {{{[(Cs,Gm),Vv],At}(Lp,Pt)},Os 36
Fig 12. Gene tree of model {{[(Gm,Vv),Cs],(Lp,Pt)},At},Os 36
Fig 13. Gene tree of model {{[(Cs,Vv),Gm)],(Lp,Pt)},At},Os 37
Fig 14. Tree models of Ludwigia palustris and Cucumis sativus. 38
Fig 15. Tree models of Ludwigia palustris and Arabidopsis thaliana 39
Fig 16. Tree models of Ludwigia palustris and Glycine max 40
Fig 17.Tree models of Ludwigia palustris and Vitis vinifera 41


附錄目錄
附錄一:流式細胞儀實驗流程 42
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