The role of transposable elements in generating functional diversity

所有生物体细胞内的DNA都含有构建和维持活体所需的基因。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所特需的，这些元素可能会以类似于计算机病毒在计算机硬盘上繁殖的方式在基因组中繁殖。这些基因元件被称为转座元件，有两种形式：使用复制粘贴机制的(第一类)和使用剪切粘贴机制的(第二类)。科学家通常认为这些元素在基因组中的存在是寄生的，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，这些可移动的元素可以对物种的进化潜力产生积极影响。例如，果蝇黑腹果蝇对有机磷农药的抗药性已经增加，这是由于在现有的较长基因中插入转座元件而产生的一种新的截短蛋白的结果。其他研究人员提出，转座子元素可能对整个生物多样性产生更深远的影响，并提出，可转座子元素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物种特别丰富。然而，到目前为止，除了确定转座元素的丰度和一组生物体的物种形成率之间的间接关系之外，几乎没有什么研究。在这项研究中，我们将集中在物种丰富的一组新热带鲶鱼，(I)它们基因组中的转座子元素含量有很大的差异，(Ii)具有不同物种形成速率的谱系，(Iii)物种形成率在距今约2500万年前突然增加，这与TE扩展大致相同。我们将首先量化不同转座子元素在Corydoras鲶鱼基因组中的丰度。这将提供不同物种中TE密度的准确估计，并通过将这些映射到系统发育框架上，将量化不同物种中TE扩展的时间。随后，我们将研究TES是否由于修复TE插入/切除位点的内在DNA修复机制而增加启动子区域的突变率。接下来，我们将调查物种形成率高的物种是否比多样性比率低的物种在基因和启动子区域插入了更多的TES。最后，我们将调查某些基因组(例如颜色模式基因)是否比其他基因(例如家务基因)受到TES的影响更大。这一建议产生的结果将使我们能够彻底调查转座元件在增加基因及其启动子区域多样性方面的作用，并为TES是否支持某些分类群中的快速物种形成提供重要证据。

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.