黄瓜（Cucumis sativus L.）是一种非常重要的经济作物，属于葫芦科（Cucurbitaceae）甜瓜属栽培种，为一年生的攀缘性草本植物。野生黄瓜（Cucumis sativus var. hardwickii）与栽培黄瓜（Cucumis sativus var. sativus L.）相比具有很多特点，如分枝性强、叶片小、果实小、坐果多、无明显主蔓、味苦、无瘤、刺稀、黑刺、不适于食用、抗逆性好、抗病等。现在普遍认为野生黄瓜是栽培黄瓜的一个变种，有可能是栽培黄瓜的野生祖先。重复序列（repetitive sequences，或称repeats）在真核生物基因组中广泛存在。重复序列最重要的组成部分为转座元件（Transposable Elements, TEs），占整个重复序列的96%左右。TEs在基因组的进化中扮演着非常重要的角色。因此，如何准确的识别和分类TEs对理解黄瓜基因组本身和TEs的结构与进化等都有非常重要的作用。在本论文中，我们使用实验室已经搭建好的基因组注释平台对栽培黄瓜和野生黄瓜两个基因组中的重复序列进行了注释。注释结果表明，黄瓜属基因组中的TEs含量达25%左右，其中栽培黄瓜的TEs含量低于野生黄瓜。栽培黄瓜基因组在人工培育过程中即有新的TEs的转座，又存在TEs的去除，且在两种力量的平衡中TEs的去除占了优势，也就是说栽培黄瓜基因组趋于缩小。通过对TEs的分类，我们发现不同类型的TEs在物种中的含量有很大差异。不论是栽培黄瓜还是野生黄瓜，其第一类反转录转座元件所占比例最高。在第一类反转录转座元件中，大部分TEs都为LTR型反转录转座元件。而在LTR型反转录转座元件中，Copia类和Gypsy类两种超家族的含量最高，且Copia类成员的数目显著大于Gypsy类。本文还对重复序列中的LTR型反转录转座元件的插入时间进行了估算。我们发现，栽培黄瓜和野生黄瓜的Copia类和Gypsy类两种超家族都在近期发生了大规模的扩增。我们对插入时间进行了统计学分析，发现它们基本分布在300万年以内，且野生黄瓜的Copia类在近期的扩增速率高于栽培黄瓜，而栽培黄瓜的Gypsy类在近期的扩增速率高于野生黄瓜。

The cucumber (Cucumis sativus L.) is a widely cultivated plant in Cucurbitaceae which is one year climbing herbs, and it’s also an economically important crop. Compared with domestic cucumber (Cucumis sativus var. sativus L.) wild cucumber (Cucumis sativus var. hardwickii) has many unique features, such as strongly branching, small leaves, small fruits, no significant main vine, bitter taste, no tumor thorns thin, black thorn, not in consumption, good stress tolerance, disease resistance etc. It is now generally agreed that wild cucumbers are a variant of domestic cucumbers and may be wild ancestors of domestic cucumbers. Repetitive sequences (repeats) are wildly existed in eukaryotic genomes. Transposable Elements (TEs) are the most important part of repeats and account for ~96% of the entire repeat sequences. TEs play a very important role in genome evolution. Therefore, the accuracy of identification and classification of TEs in the cucumber genomes is very important to understand the evolution of cucumbers and the structures of TEs. In this work, we used the genome annotation platform set up in our laboratory to identify repeats of the two cucumber genomes. The annotation results show that TEs account for ~25% of the genomes respectively. The amount of TEs in the domestic cucumber is less than in the wild cucumber. The abundance of each class of the TEs varies wildly across organisms. Among all TEs, the class I retrotransposons are the largest ones within both genomes. The majority of the known TEs are LTR retrotransposons. Of them, the Copia and Gypsy superfamilies are the most abundant in the cucumber genomes. And the number of the Copia retrotransposons is much greater than that of the Gypsy retrotransposons. We also estimated the insertion time of the LTR retrotransposons in the cucumber genomes. We found that the Copia retrotransposons and the Gypsy retrotransposons proliferated more recently in the domestic cucumber compared with them in the wild cucumber. Their insertion time is estimated to be less than 300 million years ago. Interestingly, we also found that the amplification rates of the Copia retrotransposons in the wild cucumber are higher than those in the domestic cucumber. And just the opposite, the amplification rates of the Gypsy retrotransposons in the wild cucumber are lower than those in the domestic cucumber.