臺灣博碩士論文加值系統

國際合作的水稻基因組定序工作進行多年已臻完成，各項分析工作亦相繼展開，本文採用我國負責的第五條染色體序列，利用生物資訊工具，配合適當的統計分析，探討水稻基因序列的基本特性。
本文主要包含兩個主題，一為秈稻與稉稻基因組序列之比較，以我國完成之稉稻第五條染色體基因組序列比對秈稻品種93-11的全基因組散彈槍法的草圖序列，估計此二品種第五條染色體上序列相似性。以BLAST搜尋結果，估計大約80%的序列可比對，平均相似性97%，若是去除旁系同源的比對，則有60%序列可比對，平均相似性98%。
此外也對第五條染色體基因組序列的重複序列，做一廣泛及深入探討，瞭解各種重複序列在染色體上分布，由本文之結果估計水稻第五條染色體基因組序列中約有20%以上為重複序列，其中最多的一類是轉位因子，另外有2%為短序列重複與低複雜度序列。由中節與端粒區域的分析，搜尋特定重覆序列CentO及Os48的分布範圍，分別為60kb與150kb，以303組CentO及216組Os48重複序列間的親緣分析與位置分布，推估此類連續重複的可能機制均為在附近產生重複。另外，LTR序列的相似性分析亦提供LTR-反轉位子插入基因組的演化參考，由本文結果推估LTR-反轉位子的插入並無位置上的偏好。同時，由中節與端粒重複序列的結構，可推斷第五條染色體基因組序列的完整性，目前已完成中節區域的定序，端粒區域也相當接近邊緣，顯見定序工作已克服高度重複的障礙。
這兩個工作的成果，均可提供設計高密度分子標記之參考，未來可應用於的水稻重要性狀定位與選殖，以期提高水稻品質與產量。

The IRGSP (The International Rice Genome Sequencing Program) completed a high quality sequence on schedule in December 2002. This result allows a large scale investigation on rice. We have done some detail analysis on rice chromosome 5, which sequenced by ASPGC（Academia Sinica Plant Genome Center）. This work accomplished basic characteristics of rice genome with some bioinformatics tools and combination with proper statistic approach.
This work fell into two parts. The first one was the comparison between genomic sequences of Japonica and Indica. The chromosome 5 sequences of Nipponbare were aligned with whole genome shotgun sequences of 93-11 Indica variety. The similarities between them were estimated by BLAST searching. The result revealed that the average similarity under the aligned region covered 80% of genome was 97%. After those alignments duplicated or over-dispersed were removed, 60% of genome could be aligned and the similarity was up to 98%.
The other one was the studying on repetitive sequences on rice chromosome 5. The distributions of different repetitive sequences on chromosome 5 were clarified. And details on centromere and telomere regions were featured. The differences between LTR sequences reflected the histories of insertion of retrotransposons. The completeness of centromere and telomere with highly repetitive sequences has been overcome by map-based approach.
These results are important for designing molecular markers. High density of molecular markers is the helpful tool on future breeding and genetic research of rice.

圖目錄 IV
表目錄 IX
摘要 1
第一章、前言 4
第二章、前人研究 7
第三章、稉稻第五條染色體序列與秈稻基因組序列之比較 18
一、 目的： 18
二、 材料與方法 19
(一) 資料來源與資料庫之建立 19
(二) 序列相似性分析 21
(三) 模擬試驗驗證BLAST之正確性 24
(四) BLAST結果整理與篩選 24
三、 結果 35
(一) 秈稻品種93-11基因組序列的統計性質 35
(二) BLAST結果的統計分析 39
(三) 模擬試驗的結果 47
(四) 重複比對區域的統計分析 49
四、 討論與結論 53
第四章、水稻第五條染色體基因組重複序列之分布 57
一、 目的： 57
二、 材料與方法 59
(一) 資料來源 59
(二) 重複序列資料庫比對 61
(三) 中節區域序列的重複序列 62
(四) 端粒區域的重複序列 65
(五) 中節區域及端粒區域序列的複雜度估算 66
(六) 長端重複（LTR）的序列差異分析 67
三、 結果 68
(一) 水稻第五條染色體對TIGR水稻重複序列做BLAST比對 68
(二) 水稻第五條染色體的RepeatMasker分析： 74
(三) 中節區域的重複序列分析： 84
(四) 端粒區域的重複序列分析： 90
(五) LTR-retrotransposon序列的相似性 96
(六) CentO與Os48重複序列的親緣分析 103
四、 討論與結論 109
第五章、綜合討論與結論 110
參考文獻： 117
附錄 127

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