珊瑚與渦鞭毛藻(共生藻)間的胞內共生現象是維繫珊瑚礁健康的基礎。為探究胞內共生現象建立的機轉及其背後的細胞與分子調控機轉，本研究以模式生物海葵(Exaiptasia pallida)分別接種5種同源或異源共生藻(包括clade A, B, C, D, E)，並觀察共生藻進入海葵體內後，對於海葵生長的影響及共生藻密度與分佈的時序變化，同時分別萃取接種後0小時, 12小時, 48小時, 96小時, 7日, 14日的海葵總RNA，進行26種標的基因的qPCR反應(quantitative polymerase chain reaction)，藉以驗證標的基因在海葵與同源或異源共生藻建立胞內共生過程中的表現差異，以瞭解該基因在建立胞內共生過程中所扮演的角色。結果顯示，無論是同源或異源共生藻均能進入海葵體內，但在本實驗中，僅有clade B(同源), C(異源)與D(異源)共生藻能在海葵體內存活與海葵建立共生關係，其中同源共生藻(clade B)在海葵體內的共生藻密度最高，其次依序為clade D及clade C。依據海葵底盤面積所計算的海葵生長數據顯示，在本實驗的14天期間，無論是接種同源、異源共生藻或未接種對照組的海葵大小均無顯著差異。依據NGS(next generation sequencing)分析的數據，建立共生初期(12小時, 48小時)表現大幅變化的基因數目大於後期，顯示共生藻進入海葵細胞內的初期會引起宿主基因表現的劇烈變動。本研究將這些表現量與未接種之對照組差異達10倍以上的基因進行功能分類，將其分為細胞複製周期(cell cycle)、細胞骨架(cytoskeleton)、細胞外基質(extracellular matrix)、代謝(metabolism)、緊迫反應(stress responses)與物質運送(transporter)等，並從中挑選出26種海葵標的基因，進行qPCR反應。結果顯示，在接種同源共生藻的海葵體內，各標的基因qPCR數據顯著變動的時期與NGS的數據非常相似，不僅相互驗證並呈現之前NGS數據的高準確性。此外亦發現海葵接種不同共生藻時，會有不同的基因表現變化，顯示海葵與不同的共生藻間存在特定的交互作用。整體而言，本研究驗證及篩選出參與胞內共生的相關基因，並提供分子證據以支持海葵與渦鞭毛藻建立共生的過程可分為適應期、共生藻細胞轉移期、細胞辨識時期、共生體快速複製時期及代謝調控時期等。

The endosymbiosis between corals and dinoflagellate (Symbiodinium spp.) is the basis for maintaining the health of coral reefs. In order to explore the cellular and molecular mechanisms behind the establishment mechanism of coral-dinoflagellate symbiosis, this study used 5 species of homologous or heterologous dinoflagellate (including clade A, B, C, D, E) to inoculate the model organism sea anemone (Exaiptasia pallida) and observe the influence of the dinoflagellate on the growth of the anemone after entering the anemone body, the change of density over time, and the distribution of the dinoflagellate. At the same time, we sample and extract the total RNA of the inoculated anemone at 0hr, 12hr, 48hr, 96hr, 7days, and 14 days after inoculation. The total RNA of sea anemone is used for the quantitative polymerase chain reaction (qPCR) of 26 target genes to verify the expression profile of the target gene in the process of establishing intracellular symbiosis between sea anemone and homologous or heterologous dinoflagellate, so as to understand the genes involved in the process of establishing anemone-dinoflagellate symbiosis. The results show that both homologous and heterologous dinoflagellate can enter the sea anemone, but in this experiment, only clade B (homologous), C (heterologous) and D (heterologous) dinoflagellate can establish a symbiotic relationship with anemones. Among them, the symbiot density of dinoflagellate clade B is the highest in the anemone, followed by dinoflagellate clade D and clade C. The growth of anemone as quantified by the area of the pedal disk showed that during the 14-day period of this experiment, there was no significant difference in the size of the sea anemones inoculated with homologous, heterologous dinoflagellate or uninoculated control group. According to the next generation sequencing (NGS) data, the number of genes with large changes in the initial stage of symbiosis (12hr, 48hr) was higher than in the later stage, indicating that the entry of dinoflagellate causes drastic changes in host gene expression profiles. In this study, these genes whose expression levels differed by more than 10 folds from that of the uninoculated control group were classified as the functional categories of cell cycle, cytoskeleton, extracelluar matrix, metabolism, stress responses, and molecular transporter, etc. Among them, 26 target genes were selected for qPCR reaction. The results showed that in the sea anemone inoculated with the homologous symbiotic algae, the period of significant changes in the qPCR data of each target gene was similar to the NGS data, which not only verifies each other but also attests to the high accuracy of the previous NGS data. In addition, it has also been found that when sea anemones are inoculated with different dinoflagellate, there will be different gene expression changes, indicating that there is a specific interaction between sea anemones and different dinoflagellate. In conclusion, this study verified and screened the relevant genes involved in anemone-dinoflagellate symbiosis and provided molecular evidence to support the hypothesis that the symbiosis establishment including adaptation, symbiont translocation, cellular recognition, rapid replication of symbiont and the metabolic modulation.

謝辭 I
摘要 III
Abstract V
圖頁碼 XI
表頁碼 XIII
附錄頁碼 XV
第一章、 前言 1
1.1 刺絲胞動物與共生藻之胞內共生現象 1
1.2 氣候變遷造成珊瑚白化及體內共生藻之改變 1
1.3 不同共生藻之特性及其與宿主之間的伴侶特異性 2
1.4 建立共生機轉的相關基因 3
1.5 實驗生物—美麗海葵(Exaiptasia pallida) 4
1.6 研究目的 5
第二章、 材料與方法 7
2.1 實驗策略與流程 7
2.2 實驗材料 7
2.2.1 海葵來源與培養 7
2.2.2 白化海葵製備 8
2.2.3 共生藻培養 8
2.3 共生藻品系鑑定 8
2.4.1 游離共生藻細胞取樣 8
2.4.2 游離共生藻之DNA萃取 9
2.4.3 游離共生藻之品系鑑定 9
2.3.3.1 聚合酶連鎖反應(Polymerase chain reaction, PCR) 9
2.3.3.2 限制性片段長度多態性分析(restriction fragment length polymorphism, RFLP) 9
2.3.3.3 凝膠電泳分析(agarose gel electrophoresis, AGE) 10
2.4 共生藻與海葵建立共生試驗之分析 10
2.4.1 接種試驗流程 10
2.4.2 以螢光解剖顯微鏡觀察記錄接種海葵體內之共生藻密度與分佈變化 11
2.4.3 美麗海葵體內共生藻密度之計算 11
2.4.4 海葵生長記錄 11
2.4.5 美麗海葵底盤面積計算 2
2.4.6 統計分析 12
2.5 海葵標的基因之表現量分析 12
2.5.1 標的基因之選擇及專一性引子組之設計 12
2.5.2 實驗樣本處理 13
2.5.3 總量RNA萃取及定量 13
2.5.4 反轉錄合成cDNA 13
2.5.5 即時定量PCR分析(quantitative Polymerase Chain Reaction ,qPCR ) 13
2.5.6 統計分析 14
第三章、 結果 15
3.1 培養環境參數 15
3.1.1 美麗海葵 15
3.1.2 共生藻 15
3.2 共生藻品系鑑定 .15
3.3 美麗海葵接種不同品系共生藻對海葵生長的影響 16
3.4 美麗海葵接種不同品系共生藻後之體內共生藻密度變化 16
3.4.1 美麗海葵接種不同共生藻後，體內共生藻密度之整合圖(圖10) 16
3.5 次世代定序分析美麗海葵接種同源共生藻品系B之基因表現結果 17
3.6 NGS基因及管家基因挑選及引子序列設計 19
3.7 接種實驗海葵取樣量與後續分生實驗使用量 19
3.8 控制組及不同共生藻品系之即時定量PCR基因表現結果 20
3.8.1 接種同源共生藻品系B之美麗海葵，即時定量PCR的基因表現與其基因次世代定序分析的基因表現FPKM圖譜比較。 20
3.8.2 控制組與不同共生藻品系接種之美麗海葵，在各接種時間即時定量PCR基因之表現(2-ΔΔCt)。 20
第四章、 討論 23
4.1 不同共生藻品系與美麗海葵建立共生之差異 23
4.1.1 美麗海葵接種不同共生藻品系後之生長狀況分析 24
4.1.2 美麗海葵接種不同共生藻品系後，體內共生藻密度之比較 24
4.2 美麗海葵接種同源共生藻品系B之次世代定序分析 25
4.3 美麗海葵與共生藻共生建立之主要時期 26
4.3.1 適應期—接種後12小時 26
4.3.2 共生藻細胞轉移期與細胞辨識時期—接種後48小時 27
4.3.3 共生體快速複製時期—接種後96小時 28
4.3.4 代謝調控時期—接種後第7日及14日 29
4.4 美麗海葵接種同源及異源共生藻品系間之標的基因表現比較 31
4.4. 126個標的基因選擇 31
4.4.2 在接種實驗期間，同源及異源共生藻接種美麗海葵之標的基因比較 31
第五章、 結論 37
參考文獻 39

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