橙黃壺菌 BL10 為生長在河口的真核微藻，BL10 已經被商業化使用來大
量生產 DHA、蝦紅素等物質。然而若想要更有效率利用基因體去產生這類對
於人體有效益的不飽和多碳鏈脂肪酸，就需要知道相關的基因。本研究中很大
的困難就在於 BL10 屬於未被組序過的物種，從組序、基因預測、基因體功能
註解、核糖核酸組序以及染色體套數分析都是沒有正確答案可以參考。本實驗
成功將 Illumina 和 PacBio 的資料結合並且成功組序，評估組序的正確性後，
我們也成功將基因體的序列重複區域遮蓋，進一步做基因預測以及功能性的註
解。我們成功註解出許多基因和長碳鍊不飽和脂肪酸、脂肪酸連接酶、花生四
烯酸、α-次亞麻油酸以及玉米黃素的生合成有關。另外我們將 10 小時(快速生
長期)、30 小時(油脂累積期)以及照 30 小時照藍光組分別做表現量差異的實驗，
並且發現 BL10 在 30 小時的油脂累積表現量大於 10 小時，我們也發現在 30
小時照藍光的蝦紅素相關胡蘿蔔素表現量大於 30 小時，並且這兩種現象和生
物實驗是吻合的。最後本實驗也針對 BL10 的染色體套數做了多倍體和單倍體
兩種較全面性的比較發現 BL10 是屬於二倍體，結合基因體組序、基因預測、
功能性註解和染色體套數分析結合轉錄組資料，整理成一份最佳流程。

According to previous studies, Aurantiochytrium sp. strain BL10 is a promising source of docosahexaenoic acid (DHA) and astaxanthin under certain condition. BL10 has also been used to produce large scale of DHA commercially. W have successfully unveiled genomic sequence of this non-model species through bioinformatics and identified genes that involves in many kinds of polyunsaturated fatty acid (PUFA) production. This research acquired its 59-Mbp genome, and then annotated whole genome after characterizing its genes by gene prediction. Additionally, this research has successfully categorized around 11k genes, and some of the them are found to play
significant roles in certain kinds of long chain fatty acid producing pathways like arachidonic acid (-6), alpha-linolenic acid and oleic acid (-9) by gene ontology. Moreover, the research also found many genes that are related to astaxanthin synthesis including beta-carotene synthase and zeaxanthin. Interestingly, the research has found several genes that are highly expressed under oil accumulation stage (30hrs) involving in polyunsaturated fatty acid metabolism and arachidonate CoA ligase and alpha-linolenic acid metabolism. Moreover, the research found beta-carotene and zeaxanthin related genes highly expressed under 30hrs blue light comparing to 30hrs. In the research, the research also found that BL10 belongs to diploid by comparison with different ploidy estimation tools. Last, the research will establish a customized pipeline including genome assembly, gene prediction, gene ontology, gene annotation, differential gene expression analysis and ploidy estimation which will facilitate the future studies on BL10.

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