The role of transposable elements in generating functional diversity

转座元件在产生功能多样性中的作用

• 批准号: BB/R017174/1
• 负责人: Martin Taylor
• 金额: $ 57.34万
• 依托单位: University of East Anglia
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR017174%2F1
• 关键词: role; transposable; elements; generating; functional

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.

所有生物体细胞内的DNA都含有构建和维持生物体所需的基因。然而，在大多数生物体中，基因组中还有一些不是生命所特别需要的其他成分，这些成分可能在基因组中繁殖，其方式类似于计算机病毒在计算机硬盘上繁殖。这些遗传因子被称为转座因子，有两种形式：一种是使用复制粘贴机制（I型），另一种是使用剪切粘贴机制（II型）。科学家们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可移动的元素对物种的进化潜力有积极的影响。例如，果蝇黑腹果蝇对有机磷农药的抗性已经增加，这是由于在现有的较长的基因中插入转座元件产生了一种新的截断蛋白。其他研究人员认为，转座因子可能对整个生物多样性有更深远的影响，并认为转座因子的插入可能导致进化潜力的增加，并可能解释为什么某些生物群体物种特别丰富。然而，迄今为止，除了确定转座因子的丰度与一组生物体的物种形成率之间的间接关系之外，几乎没有研究。在这项研究中，我们将重点关注一个物种丰富的新热带鲶鱼群体，它(i)在其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）在距今2500万年前物种形成率突然增加，这与TE扩张大致同时。我们将首先量化不同的转座元件的丰度在整个染色体串尾鲶鱼的基因组。这将提供不同物种TE密度的准确估计，并通过将这些映射到系统发育框架中，将量化不同物种TE扩展的时间。随后，我们将研究TE是否由于修复TE插入/切除部位的内在DNA修复机制而增加启动子区域的突变率。接下来，我们将研究高物种形成率的鲶鱼谱系是否比低物种多样化率的鲶鱼谱系在基因和启动子区域插入了更多的te。最后，我们将研究某些基因组（如颜色模式基因）是否比其他基因（如管家基因）受到TEs的影响更大。本研究结果将有助于深入研究转座因子在增加基因多样性及其启动子区域中的作用，并为te是否支持某些分类类群的快速物种形成提供重要证据。

项目成果

Removal of beneficial insertion effects prevent the long-term persistence of transposable elements within simulated asexual populations.

• DOI: 10.1186/s12864-021-07569-3
• 发表时间: 2021-04-07
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Butler CL;Bell EA;Taylor MI
• 通讯作者: Taylor MI