橙黃壺菌Aurantiochytrium limacinum BL10 是一種在台灣北部河口發現的單細胞真核微藻。其能夠產生大量的多元不飽和脂肪酸，尤其是DHA，使其極具商業價值。相比其他同樣具產油能力的微藻，BL10產油的能力更高，並且有耐高糖且耐低鹽度的特性，使其成為商業上生產藻油的有利競爭者。為了更了解 BL10 產生 DHA 的機制與優勢，本研究採用比較基因體學與轉錄體學的分析方法來找出BL10基因體與轉錄體的特徵。由於BL10是全新物種，對於基因與功能的註釋尚不清楚，故本研究第一步進行BL10的基因預測，並註釋功能。得到完整的註釋結果後，我們將同樣具產油能力的微藻與BL10進行比較基因體分析。我們發現limacinum 物種在攝取葡萄糖，產生acetyl-CoA以及對抗氧化壓力等相關基因具有更高的拷貝數，可解釋limacinum 物種有更加優秀的累積DHA能力。此外我們分析了BL10在快速生長期(10小時)與油脂累積期(30小時)基因表現量差異，並找到與DHA累積的相關基因。我們發現與高拷貝數基因相關的代謝途徑皆在30小時高表達，例如糖解反應、脂肪酸合成與抵抗活性氧反應。綜合以上分析，代表BL10製作與保護DHA的方式更有效率。本研究探討了BL10累積DHA優勢的分子機制，並為未來提升DHA產量的基因調控提供了可靠的研究方向。

Aurantiochytrium limacinum BL10 is a single-celled eukaryotic microalga found in the estuaries of northern Taiwan. It can produce large amounts of polyunsaturated fatty acids, particularly docosahexaenoic acid (DHA), making it highly valuable commercially. Compared to other oleaginous microalgal, the DHA-producing ability of BL10 is outstanding. Moreover, the ability of enduring high glucose level and low salt culture conditions makes BL10 become a favorable competitor in commercial microbial oil production. To further understand the mechanism and advantages of DHA production in BL10, we used comparative genomics and transcriptomics analysis to identify the genomic and transcriptomic features of BL10. Although the assemble genome of BL10 is available, the annotation of gene structure and function are still unclear nowadays. Therefore, the first step of this study was to predict and annotate the genes of BL10. After obtaining complete genome annotations, we applied a comparative genomic analysis between other oleaginous microalgal species and BL10. We found that limacinum strains has a higher copy number of genes related to glucose uptake, acetyl-CoA production, and repress oxidative stress, which may explain their superior ability to accumulate DHA. In addition, we analyzed the differences gene expression level between the cell division stage (10 hrs) and the oil accumulation stage (30 hrs) of BL10 and identified genes related to DHA accumulation. We found that metabolic pathways related to high copy number genes were highly expressed at 30 hours, such as glycolysis, fatty acid synthesis, and resistance to reactive oxygen species (ROS) response. Overall, this study explored the molecular mechanism behind advantages of BL10 in DHA accumulation and provided a reliable research direction of improving DHA production via gene regulation.

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邱聖博，橙黃壺菌 BL10 之全基因體及轉錄體的探討，國立成功大學生物科技與產業科學系碩士論文，2021。