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研究生(外文):Chia-Yu Huang
論文名稱(外文):Analysis of Synonymous Codon Usage in Rice Genome
外文關鍵詞:synonymous codonricebioinformatics
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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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