水稻跳躍基因分布與基因體複雜度之關聯

Genome-wide Survey of Transposable Element Insertion and Its Association with Genomic Complexity in Oryza sativa.

鄭惠玲(Hui-Ling Cheng)

指導教授 ： 趙雅婷

元智大學/工程學院/生物科技暨生物資訊研究所/碩士(2004年)

摘要

高等真核生物的基因體序列當中，有一大部份由跳躍基因所構成。水稻具有禾本科作物當中最小的基因體，跳躍基因的種類非常多而且數量豐富。由於水稻基因體和其他經濟作物的基因體具有良好的共線性，對於水稻基因體的結構分析可以增進我們對其他作物之基因體的了解。本研究使用水稻的物理圖譜、遺傳圖譜與高精確度的基因體序列資料，由全基因體的層次來探討跳躍基因分布，並且檢驗何種天擇模型適合描述水稻基因體當中跳躍基因的分布模式。我們的研究結果顯示，基因密度與反轉錄轉移子、DNA轉移子的分布具有顯著的負相關，在水稻基因體中的反轉錄轉移子與DNA轉移子的分布可以用「插入模型」來解釋。與阿拉伯芥、線蟲等適用於插入模型的模式生物不相同的是，區域重組率與水稻反轉錄轉移子的分布具有顯著的負相關，此種負相關並非只是反轉錄轉移子大量堆積於中節附近所造成的。我們也發現，跳躍基因自身的長度會影響到它們所受到之選擇壓力的大小。簡單反覆序列與反轉錄轉移子以及MITE家族的分布亦有顯著的相關關係。

關鍵字

水稻 ； 跳躍基因 ； 反轉錄轉移子 ； 重組率

並列摘要

Transposable elements (TEs) are a major component of most eukaryotic genomes. Rice genome size is the smallest among the cereal crops. Despite its small size, rice genome contains a wide variety of TEs. Rice shares synteny with other economic crops, the analysis of rice genome structure will help us to understand the genomic organization of the other crops. Using high-quality genomic sequences, physical and genetic maps as well, we analyzed the distribution of various TEs through the whole rice genome and tested the models of selection against TEs insertions. There are significant negative correlations between expressed gene density and DNA transposon/retrotransposon abundance, the results are compatible with the “Insertion model”. However, we have also found that the recombination rate is negatively associated with the abundance of retrotransposons, this distribution pattern was not found in the Arabidopsis or the C. elegans genomes. The selection pressure on insertions nearby genes appears to be lower in TEs of relative small size. The distribution of SSR is significantly correlated with the distribution of retrotransposons and MITEs.

並列關鍵字

Oryza sativa ； Transposable Element ； Retrotransposon ； Recombination rate

參考文獻

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