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研究生:黃家瑀
研究生(外文):Chia-Yu Huang
論文名稱:水稻基因體的同義編碼使用之分析
論文名稱(外文):Analysis of Synonymous Codon Usage in Rice Genome
指導教授:趙雅婷趙雅婷引用關係
學位類別:碩士
校院名稱:元智大學
系所名稱:生物科技與工程研究所
學門:生命科學學門
學類:生物科技學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:42
中文關鍵詞:同義編碼水稻生物資訊
外文關鍵詞:synonymous codonricebioinformatics
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同一基因體中的不同基因,或是不同的基因體之間,選擇同義編碼的形式會有所不同。對於原核生物和真核生物來說,影響編碼使用偏好的因素不盡相同。本研究分析水稻基因體的編碼使用偏好,並探討在兩種品種、三種不同組織當中,水稻基因之表現量和編碼使用偏好之間的關係。密碼子第三位置的GC含量與編碼偏好有高度相關。此外,具有高度編碼偏好的基因其表現量顯著高於低度編碼偏好的基因。本論文並進一步分析高度編碼偏好之基因功能並進行分類。
Patterns of synonymous codon usage vary among genes within a genome and different genomes as well. It is called codon usage bias when the amino acids show the preference for particular nucleotide at the third position of codons. In eukaryotes the codon usage bias is very complicated, and it is associated with many biological factors. This research analyzes the codon usage patterns in rice genome, as well as the relationship between the gene expression levels and the codon usage bias. The results show that there is significant correlation between the GC3 content and the measurements of codon usage bias. The higher the GC3, the stronger the codon usage bias is. Besides, higher-codon-bias genes expressed at significantly higher level than lower-codon-bias genes do. The biological functions and cell localizations of the high-codon-bias genes were assessed based on the Gene Ontology analysis.
圖目錄 ix
表目錄 x
一、序論 1
1.1 研究背景 1
1.2 研究動機與目的 2
二、前人研究 3
2.1 酵母菌、果蠅及線蟲編碼使用偏好之研究 3
2.2 哺乳類動物編碼使用偏好之研究 3
2.3 植物編碼使用偏好之研究 4
三、編碼偏好分析方法 6
3.1 相對同義編碼使用值 6
3.2 有效密碼子數 6
3.3 密碼子適應指數 7
四、實驗資料與研究方法 9
4.1 基因晶片資料 9
4.2 cDNA序列、mRNA序列及CDS 9
4.3 探針和基因的對應 10
4.4 編碼使用偏好之評估 13
五、結果與討論 14
5.1 探針序列和基因的對應 14
5.2 水稻基因之編碼偏差分析結果 16
5.3 基因表現量與編碼偏差之關係 31
5.4 高編碼偏差之基因功能分析 32
六、結論 38
參考文獻 39
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