How does ploidy level impact repetitive DNA? Insights from di-, tetra- and hexaploid populations of Orobanche gracilis

核糖体rRNA基因、卫星DNA和分散的可移动遗传元件等重复序列在植物基因组进化中发挥着重要作用。这是由于它们对基因组大小（它们是基因组大小增加的主要贡献者）、基因进化、基因调控和基因表达的影响。尽管具有这种重要作用，但我们对不同重复DNA类型对植物基因组进化的个体贡献知之甚少。我们将应用454焦磷酸测序来表征一组非光合开花植物的重复DNA，这些植物显示出不同的基因组动力学。先前对全寄生的orobche和Phelipanche的研究表明，它们在倍性水平、核基因组大小范围和逆转录因子多样性方面存在差异。我们将通过比较四种Orobanche和三种Phelipanche来验证这一假设，即这主要是由于它们的重复DNA片段。具体来说，我们将确定在(i)不同年龄的物种群体中负责基因组分化的重复DNA的种类，（ii）宿主范围狭窄的物种与广泛的物种，（iii）多年生物种与一年生物种，以及（iv）二倍体与多倍体物种。新一代测序技术已经被证明能够成功地解决这类问题。这个项目的主要新颖之处在于广泛的比较背景，这将允许评估进化趋势。Orobanche和相关属的所有成员都是全息寄生虫，其中一些已被证明含有水平转移的基因，这进一步有助于评估逆转录转座子在HGT中的作用。

Repetitive sequences, such as ribosomal rRNA genes, satellite DNA, and dispersed mobile genetic elements, play an essential role in plant genome evolution. This is due to their effects on genome size (they are main contributors to genome size increases), gene evolution, gene regulation, and gene expression. Despite this essential role, we know little about the individual contributions of different repetitive DNA types to plant genome evolution. We will apply 454 pyrosequencing to characterize repetitive DNA in a group of nonphotosynthetic flowering plants that show contrasting genome dynamics. Previous work on the holoparasitic Orobanche and Phelipanche has shown that they differ in ploidy levels, range of nuclear genome sizes, and retroelement diversity. We will test the hypothesis that this is mainly due to their repetitive DNA fractions by comparing four species of Orobanche and three of Phelipanche that exemplify these differences. Specifically, we will identify the kinds of repetitive DNA responsible for genome differentiation in (i) species groups of different ages, (ii) species with narrow vs. wide host ranges, (iii) perennial vs. annual species, and (iv) diploid vs. a polyploid species. Next-generation sequencing technology has already proven successful to address these types of questions. The primary novelty of this project is the broad comparative context, which will allow assessing evolutionary trends. That all members of Orobanche and related genera are holoparasites and that some have been shown to harbor horizontally transferred genes furthermore may allow assessing the role of retrotransposons in HGT.