description
- 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.