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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 呂俊毅(Jun-Yi Leu) | |
dc.contributor.author | Yu-Hsuan Cheng | en |
dc.contributor.author | 鄭毓鋗 | zh_TW |
dc.date.accessioned | 2021-06-16T16:13:11Z | - |
dc.date.available | 2023-06-05 | |
dc.date.copyright | 2020-06-05 | |
dc.date.issued | 2020 | |
dc.date.submitted | 2020-05-29 | |
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dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/62872 | - |
dc.description.abstract | 內共生是在不同品系的真核生物演化過程中常見並且重要的推動力之一,然而,內共生在初始階段是如何形成以及宿主與共生個體如何形成穩定內共生關係的過程卻仍不是很清楚。因此,我們決定使用草履蟲以及綠藻作為研究物種來探討初始內共生關係的分子機制,Paramecium bursaria是在草履蟲屬中較早分化並且是在草履蟲屬中惟二可以和綠藻形成共生關係的物種,過去研究雖然有觀察到草履蟲與綠藻建立內共生關係時,綠藻在草履蟲胞內的分布變化以及諸如光線或是光合作用抑制劑等因素會影響內共生形成,但是對於有哪些基因參與調控這個現象卻仍不清楚。為了了解有哪些基因參與調控,我們首先定序組裝了高品質的基因體並且結合了不同族群的基因體進行註解,我們發現基因體當中有一些蛋白質及基因家族的擴增可能和內共生現象有關,而藉由基因體分析我們也觀察到在該物種大核發育時的染色體重組現象有別於其他纖毛蟲,並且造成基因體中基因間的拷貝數差異極大,而細胞可能會藉由調控特定基因拷貝數以適應環境。接著,我們結合了基因體分析以及比較帶有共生綠藻及未帶有共生綠藻的宿主轉錄組分析篩選出可能和內共生調控相關的基因,並且進一步建立基因干擾技術以供未來驗證所需。另一方面,我們也發現不同品系的宿主能夠建立共生關係的綠藻物種及能力不同,我們也定序比較了不同宿主的基因體以尋找和共生現象相關的基因。最後,我們也發現共生關係能夠使得宿主對於致病菌有更高的抗性。綜合以上,由我們的實驗結果發現在草履蟲基因體大規模的基因體拷貝數差異可能是一種幫助細胞適應環境的原始機制,而基因體的完善以及其後的轉錄體分析及實驗數據則為了內共生機制研究建立了基石。 | zh_TW |
dc.description.abstract | Endosymbiosis is one of the major forces driving the evolution of eukaryotic cells, which has occurred multiple times in different lineages during evolutionary history. However, the initial process of how the endosymbiosis is formed and established in the host cell is still unclear. Here, we use the ciliate Paramecium bursaria and the algae Chlorella spp. to study the early stage of endosymbiosis. Paramecium bursaria is a highly divergent species of the genus Paramecium, which can stably establish endosymbioses with green algae. Previous studies have shown that some key cytosolic events establish endosymbiosis. However, the molecular mechanisms or genes responsible for initiating and establishing the relationship between P. bursaria and Chlorella spp. remain largely unknown. To address this question, we first assembled a high-quality macronuclear genome of P. bursaria and further defined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that were potentially associated with endosymbiosis. Moreover, we observed a unique chromosome breakage pattern that resulted in a highly variable gene dosage throughout the genome and found it may allow cells to adjust gene copy numbers globally according to individual gene functions. After we acquired the genome content of P. bursaria, we combined both genomic and transcriptomic data of symbiotic and aposymbiotic cells to select candidate genes that may play a role in the general process of endosymbiosis and further set up an RNAi feeding experiment in P. bursaria for validation. On the other hand, we also found P. bursaria strains exhibited different abilities to establish stable endosymbiosis with different Chlorella species and strains. The genomic data of those P. bursaria strains were analyzed to identify candidate genes contributing to this difference. Finally, we investigated the possible benefits of this symbiotic relationship and found that symbiotic cells are more resistant to a pathogenic bacterium than the aposymbiotic cells. Above all, our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments and shed light on the genetic basis of endosymbiosis establishment. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T16:13:11Z (GMT). No. of bitstreams: 1 ntu-109-D02b48008-1.pdf: 3066872 bytes, checksum: 234f1eec2f6cbb1457b9b9672abfc4ba (MD5) Previous issue date: 2020 | en |
dc.description.tableofcontents | 口試委員會審定書 I
Acknowledgements II Chinese Abstract III English Abstract IV Table of Contents VI List of Figures VIII List of Tables X Chapter I: Population genomics reveals genome plasticity in Paramecium bursaria 1 I-1 Introduction 2 I-2 Results 5 I-2-1 A global view of the Paramecium bursaria macronuclear genome 5 I-2-2 Protein family expansion and gene duplication in Paramecium bursaria 7 I-2-3 High heterogeneity of macronuclear minichromosome structures 9 I-2-4 Extensive copy number variation in the macronuclear genome 10 I-2-5 Copy number variation is regulated according to gene function 11 I-3 Discussion 13 I-4 Conclusion 17 I-5 Figures 18 I-6 Tables 42 Chapter II: Identification of the Paramecium bursaria genes involved in endosymbiosis with Chlorella spp. 56 II-1 Introduction 57 II-2 Results 59 II-2-1 Identification of candidate genes involved in endosymbiosis using both genomic and transcriptomic data 59 II-2-2 The RNAi feeding method could be used to knockdown gene expression in Paramecium bursaria 60 II-2-3 The infectivity of different Chlorella species with four P. bursaria strains are different 61 II-2-4 The endosymbiont can protect the host from pathogen invasion 62 II-3 Discussion 64 II-4 Conclusion 66 II-5 Figures 67 II-6 Tables 74 Materials and Methods 85 Reference 95 | |
dc.language.iso | en | |
dc.title | 探討草履蟲與綠藻共生之分子機制 | zh_TW |
dc.title | Molecular mechanisms of endosymbiosis between
Paramecium bursaria and Chlorella spp. | en |
dc.type | Thesis | |
dc.date.schoolyear | 108-2 | |
dc.description.degree | 博士 | |
dc.contributor.coadvisor | 莊樹諄(Trees-Juen Chuang) | |
dc.contributor.oralexamcommittee | 蔡怡陞(I-Sheng Jason Tsai),于宏燦(Hon-Tsen Yu),姚孟肇(Meng-Chao Yao),周睿鈺(Jui-Yu Chou) | |
dc.subject.keyword | 纖毛蟲,草履蟲,拷貝數變異,計畫性染色體重組,比較基因體學,內共生,綠藻, | zh_TW |
dc.subject.keyword | ciliate,Paramecium,copy number variation,programmed DNA rearrangement,comparative genomics,endosymbiosis,algae, | en |
dc.relation.page | 104 | |
dc.identifier.doi | 10.6342/NTU202000883 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2020-05-29 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 基因體與系統生物學學位學程 | zh_TW |
顯示於系所單位: | 基因體與系統生物學學位學程 |
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