蕓苔屬(Brassica)不僅包含許多重要的作物，更是研究基因體演化的理想模型。本 論文的目的是為瞭解蕓苔屬基因體重複序列的演化歷史以及熱逆境調控重複序列表 現的機制。首先，我們開發系統性的轉座子(TE, transposable element)註解系統， 對蕓苔屬 U 三角中的六種植物做了轉座子、核醣體 DNA(rDNA)和中心粒 (centromere)重複序列的註解。我們發現 B. oleracea 基因體在大約 150 萬年前有一 個第一型轉座子超級家族(class-I TE superfamily):Gypsy 大量表現並複製的現 象。我們還在二倍體和四倍體蕓苔屬物種的 C 染色體中發現了大量複製的一個第二 型轉座子超級家族(class-II TE superfamily): CACTA。另外，我們在 C 染色體中 發現了新的 5S rDNA 拷貝，也用 SNP(single nucleotide polymorphism)分析辨識出 了 A 染色體中的兩個 5S 核醣體型。由 45S rDNA 的二級結構分析發現在蕓苔屬的 A、B 和 C 染色體中，ITS1(internal transcribed spacer 1)比 ITS2 具有更高的序列岐 異度。為了找出 B. oleracea 中與逆境相關的轉座子家族(TE family)，我們依據序 列相似性進一步將轉座子分類為轉座子家族。我們在 B. oleracea 中鑑定出了具有根 特異性且會被熱誘導的 ONSEN 轉座子表現。這個 ONSEN 家族的熱響應因子 (HRE，heat responsive element)不具功能性，且鄰近區域處都存在兩種保守序 列。此保守序列的功能還需要被進一步研究。 總結來說，本論文對重複序列做註釋 有助於更全面地對重複序列在蕓苔屬進行種間和種內的比較。

Brassica genus contains many important crops and is an idea model to study genome evolution. Here, we aim to understand the evolutionary history of Brassica genomes and the impacts of repetitive sequences in response to heat stress. We first characterized the profiles of transposable elements (TEs), ribosomal DNAs (rDNAs) and centromeric repeats in six species of Brassica U’s triangle of A, B, C genome karyotypes. We have developed a TE annotation system and systemically analyzed published Brassica genome. In particular, we have identified bursts of Gypsy, a class-I TE superfamily, around 1.5 million years ago in B. oleracea genomes. We have also found high copy number of CACTA, a class-II TE superfamily, in diploid and polyploid species of Brassica C genomes. Novel 5S rDNA copies were identified in C genome, and SNP analysis have characterized two 5S ribotypes in A genome. Secondary structure analysis of 45S rDNA showed more divergence in ITS1 (internal transcribed spacer) than ITS2 across A, B and C genomes. We further classified TEs into families based on the sequence similarity. We identified a class of root-specific heat-induced ONSEN expression in B. oleracea. This ONSEN family in B. oleracea genomes carries two conserved motifs that are proximal to the non-functional heat responsive element (HRE) and the function of the motifs requires further examination. Taken together, this annotation system enables a more comprehensive investigation of repetitive sequence dynamics in an interspecies and intraspecies scale of Brassica genus.

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