The role of transposable elements in generating functional diversity

所有生物体细胞内的DNA都含有构建和维持生命体所需的基因。然而，在大多数生物体中，基因组的其他组成部分并不是生命特别需要的，这些元素可以在基因组中以类似于计算机病毒在计算机硬盘上繁殖的方式繁殖。这些遗传因子被称为转座因子，有两种形式：使用复制和粘贴机制的转座因子（I型）和使用剪切和粘贴机制的转座因子（II型）。科学家通常认为基因组中这些元素的存在是寄生的，它们对宿主的影响要么是中性的，要么是负面的。然而，人们越来越认识到，这些移动的因素可以对一个物种的进化潜力产生积极的影响。例如，果蝇Drosophila melanogaster对有机磷农药的抗性已经增加，这是由于在现有的较长基因中插入转座因子而产生的新型截短蛋白质的产生。其他研究人员认为转座因子可能对整个生物多样性产生更深远的影响，并认为转座因子的插入可能会导致进化潜力的增加，并可能解释为什么某些生物群体特别丰富。然而，到目前为止，几乎没有研究，超越了确定转座因子的丰度和一组生物的物种形成率之间的间接关系。在本研究中，我们将集中研究一个物种丰富的新热带区鲶鱼群，它们（i）在基因组的转座因子含量上有相当大的差异，（ii）具有不同物种形成率的谱系，（iii）物种形成率突然增加。我们将首先对不同转座因子的丰度进行量化，在鲶科鱼类的基因组中。这将提供不同物种中TE密度的准确估计，并且通过将这些映射到系统发育框架上，将量化不同物种中TE扩增的时间。随后，我们将研究TE是否会增加启动子区域的突变率，作为修复TE插入/切除位点的内在DNA修复机制的结果。接下来，我们将调查是否鲶鱼血统与高物种形成率有更多的TE插入基因和启动子区域比物种低多样化率。最后，我们将研究某些基因组（例如颜色模式基因）是否比其他基因（例如管家基因）更受TE的影响。在这个建议中产生的结果将允许转座因子在增加基因及其启动子区域的多样性的作用进行彻底的调查，并提供重要的证据，以TE是否支持快速物种形成的一些分类组。

The DNA housed inside the cells of all organisms contains the genes required for building and maintaining living bodies. However, in most organisms, there are other components of the genome that are not specifically required for life and these elements may multiply within the genome in a manner similar to computer viruses multiplying on a computer hard-drive. These genetic elements are known as transposable elements and come in two forms: those which use a copy and paste mechanism (type I) and those that use a cut and paste mechanism (type II). Scientists have typically viewed the presence of these elements in genomes as parasitic and their effects on the host as either neutral or negative. However, it is increasingly recognised that these mobile elements can have a positive effect on the evolutionary potential of a species. For example, the resistance of the fruit fly Drosophila melanogaster to an organophosphate pesticide has increased as a result of the production of a novel truncated protein generated by the insertion of a transposable element in an existing longer gene. Other researchers have suggested that transposable elements may have more profound impacts on biodiversity as a whole and have suggested that the insertion of transposable elements may lead to increased evolutionary potential and may explain why some groups of organisms are particularly species rich. However, to date there has been little research that goes beyond identifying a circumstantial relationship between the abundance of transposable elements and the speciation rates of a group of organisms. In this study, we will focus on a species rich group of Neotropical catfishes that (i) have considerable differences in the transposable element content of their genomes and (ii) have lineages with different rates of speciation and (iii) show a sudden increase in speciation rate ~25 million year before present which is broadly contemporaneous with the TE expansion.We will firstly quantify the abundance of different transposable elements across the genomes of Corydoras catfishes. This will provide an accurate estimate of the TE density in different species, and by mapping these onto a phylogenetic framework, the timing of TE expansions in different species will be quantified. Subsequently, we will investigate whether TEs increase the mutation rates of promoter regions as a result of the intrinsic DNA repair mechanisms that heal TE insertion / excision sites. Next we will investigate whether catfish lineages with high speciation rates have more TEs inserted in genes and promoter regions than species with low diversification rates. Finally, we will investigate whether certain groups of genes (e.g. colour pattern genes) have been more greatly affected by TEs than other genes (e.g. housekeeping genes). The results generated in this proposal will allow a thorough investigation of the role of transposable elements in increasing the diversity of genes and their promoter regions and provide important evidence as to whether TEs underpin rapid speciation in some taxonomic groups.