Ribosomal DNA variation in multi-locus systems

最近的技术进步导致获得选定生物体基因组序列的成本和时间大幅下降。因此，目前世界各地正在对数千种生物的基因组进行测序。一旦获得这些基因组序列，研究人员就可以使用不断增长的软件工具包进行分析。分析这些序列的大部分努力自然都花在了检测基因上，这些基因制造了用于细胞生长和发育的蛋白质。尽管现在公开的基因组序列数量很多，但其中一部分很少受到关注，那就是核糖体DNA（rDNA）。rDNA是生命所必需的，因为它参与“阅读”基因序列，并从该序列构建蛋白质。rDNA本身是一个很短的序列（只有几千个“字母”长），在许多生物体中，它在基因组的一个或多个位置上以数十或数百个拷贝的形式重复。直到最近，研究人员还认为单个生物体中的所有数十或数百个rDNA拷贝都是相同的。然而，最近的研究表明，rDNA拷贝之间确实存在差异，无论是拷贝数量还是其DNA序列。此外，rDNA现在被证明在衰老等重要的生物过程中发挥作用，但我们还没有发现这些rDNA差异如何影响这些过程。在过去的十年中，我们仔细分析了酵母物种中的rDNA，这些酵母物种将其包装在基因组中的一个单一位置。我们已经证明，生物体内部和生物体之间rDNA拷贝之间的差异包含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，我们将扩展我们的rDNA差异的知识，包括物种，组织他们的rDNA在两个或两个以上的基因组位置。我们将通过分析特殊的序列数据集来做到这一点，这些数据集只包含基因组中的一条染色体-类似于一本书中的一个章节-用于酵母物种光滑念珠菌（2个rDNA位置）和面包小麦（5个rDNA位置）。这样的分析很重要，因为人类依赖的许多物种，包括农场动物和谷类作物，在多个地点组织它们的rDNA，找出rDNA在不同地点之间的差异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位置的生物体产生广泛的影响。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，而无需我们通过眼睛编辑其结果。然后，我们将确定我们已经确定的rDNA差异实际上被酵母和小麦用于构建蛋白质。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生物体生活的环境条件（例如温度，水的可用性）。这些结果可能表明rDNA差异改变了生物体的功能（即其性状），将被传达给相关的作物和酵母改良项目，旨在开发针对特定目的的新品种和菌株（例如在某些环境条件下生长最好的作物）。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，以使世界各地的研究人员受益，以便其他人可以对rDNA变异，进化和功能进行自己的研究。

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.