Ribosomal DNA variation in multi-locus systems

最近的技术进步使获取所选生物的基因组序列的成本和时间都大幅下降。因此，目前世界各地正在对数千种生物的基因组进行测序。一旦获得了这些基因组序列，研究人员就可以使用越来越多的软件工具包对其进行分析。分析这些序列的大部分工作自然都花在了检查基因上，这些基因产生的蛋白质用于细胞的生长和发育。尽管现在公开的基因组序列数量很多，但其中一个受到关注的部分是核糖体DNA(RDNA)。RDNA对生命来说是必不可少的，因为它参与“读取”基因序列，并从该序列构建蛋白质。RDNA本身是一个短序列(几千个“字母”的长度)，在许多生物体中，它在基因组的一个或多个位置以数十或数百个副本反复重复。直到最近，研究人员还认为，单个生物体内rDNA的数十个或数百个拷贝是完全相同的。然而，最近的研究表明，rDNA拷贝之间确实存在差异，无论是在拷贝数方面还是在它们的DNA序列方面。此外，rDNA现在被证明在重要的生物过程中发挥作用，例如衰老，但我们还没有发现这些rDNA差异如何影响这些过程。在过去的十年里，我们仔细地分析了各种酵母中的rDNA，这些酵母将rDNA包装在它们基因组中的一个位置。我们已经证明，生物内部和生物之间的rDNA副本之间的差异封装了丰富的进化信息来源。这项工作的一个重要部分是开发两个软件工具：turnip和VariantLister，使我们能够找到这些rDNA差异。在这里，我们将扩展我们对rDNA差异的知识，以包括跨两个或更多基因组位置组织rDNA的物种。我们将通过分析酵母物种光滑假丝酵母(2个rDNA位置)和面包小麦(5个rDNA位置)的特殊序列数据集来实现这一点，这些数据集仅包含基因组中的单个染色体-类似于书中的一章。这样的分析很重要，因为许多人类赖以生存的物种，包括农场动物和谷类作物，都会在多个地点组织它们的rDNA，并找出不同地点rDNA的差异，这可能有助于我们在未来开发更好的品种和品种。然后，我们将测试我们是否真的可以使用整个基因组的DNA序列来确定相同的信息，这将对我们未来如何分析具有多个rDNA位置的生物具有广泛的影响。这些任务将要求我们首先改进VariantLister软件，以便它可以准确地找到rDNA差异，而不需要我们用眼睛编辑它的结果。然后，我们将确定我们所鉴定的rDNA差异实际上被酵母和小麦用来构建蛋白质。特别是，我们将发现它们使用的rDNA差异是否取决于它们被发现的基因组位置和有机体生活的环境条件(例如温度、水的可用性)。这些结果可能表明rDNA差异改变了生物体功能的某些方面(即其特征)，这些结果将被传达给旨在开发针对特定目的(例如，在某些环境条件下生长得最好的作物)的新品种和菌株的相关作物和酵母改良项目。最后，我们将在一个专门的项目网站上免费提供所有项目数据集和VariantLister工具，使世界各地的研究人员受益，以便其他人可以开展自己的rDNA变异、进化和功能研究。

Recent technological advances have led to a dramatic drop in both the cost and the time taken to obtain the genome sequence of a chosen organism. As a consequence, the genomes of thousands of organisms are currently being sequenced around the world. Once these genome sequences have been obtained, researchers may then analyse them using a growing toolkit of software. Much of the effort analysing these sequences is naturally spent on examining the genes, which make proteins that are used in cells for growth and development. Despite the quantity of genome sequences now publicly available, one part of them that has received scant attention is the ribosomal DNA (rDNA). The rDNA is essential for life, as it is involved in "reading" the sequence of a gene and from that sequence constructing a protein. The rDNA itself is a short sequence (of a few thousand "letters" long) that in many organisms is repeated over and over again, in tens or hundreds of copies, at one or more locations within a genome. Until recently, researchers believed that all the tens or hundreds of copies of the rDNA within a single organism were identical. However, recent studies have shown that there are indeed differences between rDNA copies, both in terms of the number of copies and their DNA sequences. Furthermore, the rDNA is now being shown to play a role in important biological processes such as ageing but we have yet to discover how these rDNA differences affect such processes. Over the last decade, we have meticulously analysed the rDNA in species of yeast that package it within just a single location within their genome. We have shown that the differences between copies of the rDNA both within and between organisms encapsulate a rich source of evolutionary information. An important part of this work was developing two software tools, TURNIP and VariantLister, that enabled us to find those rDNA differences. Here, we will extend our knowledge of rDNA differences to include species that organise their rDNA across two or more genomic locations. We will do this by analysing special sequence datasets that comprise just a single chromosome within a genome - analogous to a chapter within a book - for the yeast species Candida glabrata (2 rDNA locations) and bread wheat (5 rDNA locations). Such an analysis is important as many species that humans depend upon, including farm animals and cereal crops, organise their rDNA across multiple locations and finding out how the rDNA differs between locations may help us to develop better breeds and varieties in the future. We will then test whether we could in fact have used DNA sequences from whole genomes to determine the same information, which will have broad implications for how we analyse organisms with multiple rDNA locations in the future. These tasks will require us to first improve the VariantLister software so that it can accurately find rDNA differences without the need for us to edit its results by eye. We will then determine which of the rDNA differences that we have identified are actually used by yeast and wheat to construct proteins. In particular, we will discover if the rDNA differences they use depend on the genomic location at which they are found and the environmental conditions in which the organism is living (e.g. temperature, water availability). These results, which may indicate rDNA differences that change aspects of how an organism functions (i.e. its traits), will be communicated to relevant crop and yeast improvement projects that are aiming to develop new varieties and strains tailored to specific purposes (e.g. crops that grow best in certain environmental conditions). Finally, we will make all project datasets and the VariantLister tool freely available on a dedicated project website, to the benefit of researchers around the world, so that others may carry out their own studies on rDNA variation, evolution and function.