研究生: |
李宜謙 Lee, Yi-Chien |
---|---|
論文名稱: |
線蟲比較基因體學 Comparative genomics of free-living nematodes |
指導教授: |
蔡怡陞
Tsai, Isheng |
口試委員: |
蔡怡陞
Tsai, Isheng 莊樹諄 Chuang, Trees-Juen 楊姍樺 Yang, Shan-Hua 顧銓 Ku, Chuan 駱乙君 Luo, Yi-Jyun |
口試日期: | 2023/09/19 |
學位類別: |
博士 Doctor |
系所名稱: |
生物多樣性國際研究生博士學位學程 Taiwan International Graduate Program on Biodiversity |
論文出版年: | 2023 |
畢業學年度: | 112 |
語文別: | 英文 |
論文頁數: | 97 |
英文關鍵詞: | Free-living nematode, nematode community, nematode genomics, whole genome amplification, de novo genome assembly |
研究方法: | 實驗設計法 |
DOI URL: | http://doi.org/10.6345/NTNU202301786 |
論文種類: | 學術論文 |
相關次數: | 點閱:71 下載:0 |
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Over 70% of nematode species are free-living. They are found in a wide variety of habitats and are essential for maintaining microenvironments. However, studies on nematodes have mainly focused on parasites and terrestrial free-living. Free-living nematodes in aquatic ecosystems represent 50% of all nematode species but are poorly understood. Recently, studies of marine free-living nematodes have focused on their potential to address nematode phylogeny questions and explore the evolution of nematode parasitism and adaptation to extreme environments. My Ph.D. aims to sequence the genome of a marine free-living nematode to reconstruct nematode phylogeny and compare it with published nematode genomes to investigate nematode genome diversity. During the sampling process, I analyzed the nematode community around the northern coast of Taiwan. It is important to note that marine nematode species are not amenable to axenic culture under laboratory conditions. To alleviate this issue, I utilized multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA from one individual, respectively. We evaluated the bias of this protocol using Caenorhabditis elegans. While reduced genome coverage was detected in repetitive regions, we generated assemblies that covered 98% of the reference genome using long-read sequences produced with Oxford Nanopore Technologies (ONT). Annotation of the sequenced transcriptome and available assemblies showed that gene predictions were more precise, comprehensive, and contained fewer false positives than de novo transcriptome assembly methods. Our results demonstrate the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
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