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研究生:莊梓弘
研究生(外文):Tzu-HungChuang
論文名稱:赤箭種類中真菌組成之描述
論文名稱(外文):Characterization of fungal compositions in Gastrodia species
指導教授:劉宗霖劉宗霖引用關係
指導教授(外文):Tsung-Lin Liu
學位類別:碩士
校院名稱:國立成功大學
系所名稱:生物資訊與訊息傳遞研究所
學門:生命科學學門
學類:生物訊息學類
論文種類:學術論文
論文出版年:2016
畢業學年度:104
語文別:中文
論文頁數:67
中文關鍵詞:蘭科赤箭共生真菌
外文關鍵詞:orchidGastrodiasymbiotic fungi
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赤箭為特殊的無葉綠素蘭科植物,須依賴共生真菌提供養分來生存,因此我們預期赤箭的空間分布會受到環境中真菌種類的限制。雖然有這層限制,卻有部分赤箭能生長於不同環境中。基於赤箭對真菌的依賴性,我們推測能適應不同的環境真菌組成最有可能與赤箭能否廣泛分佈有關。在過去僅發現分布較侷限且稀有的赤箭具有特異共生的單一優勢共生真菌,卻沒有關於廣泛分佈赤箭相關的真菌研究。於本次研究中,我們取廣泛分佈的爪哇赤箭與稀有分布的夏赤箭,藉由Illumina定序其根部以及周圍土壤中的所有28S DNA,由此定序資料做物種鑑定與樣本間真菌組成差異的比較。我們使用28S定序資料比對回NCBI LSU資料庫後,鑑定出夏赤箭植株中以Mycena為優勢物種;與此相對,爪哇赤箭植株則以多樣的真菌存在於根內為特徵,且沒有明顯的優勢物種。爪哇赤箭植株的多樣性皆高於夏赤箭。於進一步追蹤後,我們證實爪哇赤箭根部內的真菌菌相會受到其周圍土壤真菌所影響,且相對於夏赤箭根部與土壤真菌組成而言,我們發現爪哇赤箭的根部與土壤的真菌菌組成關係確實相對類似。這些證據說明爪哇赤箭能夠讓更多土壤真菌較無限制的進入根內,並且對於真菌的選擇較不挑剔。這些現象也能解釋兩種赤箭分布範圍的差異狀況。
Gastrodia is a special chlorophyll lacking plant and relies on specific symbiotic fungi for nutrients. Therefore, environmental fungi can limit the spatial distribution of Gastrodia. Under this constraint, however, some Gastrodia species are still widely distributed. We hypothesize that symbiotic fungal composition is an important factor for a Gastrodia specie to be widespread or endemic. It has been reported that only few specific fungi are present in endemic Gastrodia species, e.g., elata and flavilabella. However, there is still no report about fungi in widespread Gastrodia species. In this study, we collected two Gastrodia species, widespread Gastrodia javanica and endemic Gastrodia flavilabella. After extracting total DNAs from tubers and soils of the two Gastrodia species, 28S rDNA sequencing was applied for species identification. We found that Mycena dominated in the tubers of G. flavilabella while different fungi lived in the tubers of G. javanica. Consistently, fungal diversity was higher in the G. javanica tubers than in the G. flavilabella tubers. In addition, dominating fungi in different G. javanica individuals were different. This suggests that the widespread G. javanica is less limited by specific symbiotic fungi.
中英文摘要 I
誌謝 VI
目錄 VII
表目錄 X
圖目錄 XI
符號 XII
第一章 緒論 1
1-1. 蘭科植物 1
1-2. 無葉綠素蘭 1
1-3. 赤箭的特性 2
1-4. 共生真菌的重要性 3
1-5. 共生菌與植物稀有度的關係 4
1-6. 本文動機與目標 5
第二章 材料與方法 6
2-1. 赤箭樣本的蒐集 6
2-2. 定序樣本的處理 8
2-3. 定序結果的過濾與整理 9
2-4. 資料庫中序列的蒐集 10
2-5. 鑑定物種工具與分析方法 10
2-6. 物種序列分群與分析方法 11
2-6-1. 操作型物種分群 12
2-6-2. 親緣樹和主成分分析 13
2-7. 統計分析方法 14
第三章 實驗結果與分析 15
3-1. 緒論 15
3-2. 定序資料 16
3-3. 真菌擴增子的長度分布 18
3-4. 操作型物種分群數量 20
3-5. 赤箭間物種多樣性差異 22
3-6. 樣本的相似度分析 25
3-6-1. 親緣樹 26
3-6-2. 主成分分析結果 27
3-7. 夏赤箭與爪哇赤箭物種鑑定結果 28
3-7-1. 門 (Phylum) 29
3-7-2. 綱 (Class) 30
3-7-3. 目 (Order) 31
3-7-4. 科 (Family) 32
3-7-5. 屬 (Genus) 34
3-7-6. 種 (Species) 35
3-7-7. 操作型物種分群之分類結果(OTU classification) 36
3-8. 植株-土壤真菌菌相間的關係 37
3-8-1. 植株-土壤的真菌組成相關性 38
3-8-2. 文氏圖(Venn_diagram) 41
3-8-3. 小結 42
第四章 討論 43
4-1. 序列數量的充分性 43
4-2. 真菌引子的效率 45
4-3. 加權與未加權物種數量對於分析結果的差異 47
4-3-1. 加權與未加權親緣樹 48
4-3-2. 加權與未加權主成分分析 50
4-3-3. 小結 51
4-4. 物種多樣性指標的選擇 51
4-5. 在赤箭根內存在的物種 54
4-6. 赤箭真菌特性的比較 56
第五章 結論 57
第六章 未來展望 58
第七章 參考文獻 59
第八章 附錄 62
8-1. 各樣本前十名操作型物種分類結果 62
8-2. 僅在植株中發現的真菌 67
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