Exploring the transcriptome of Aspergillus nidulans

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For many organisms, ranging from pathogenic bacteria to humans, their DNA content, the genome, has been sequenced. This is a marvellous tool for us to improve our understanding of biology with far reaching consequences in fighting human disease, safeguarding and enhancing food production, developing new sources of energy and producing a wide array of products we need, ranging from medicines to fine chemicals. However, the usefulness of these genome sequences is limited by our understanding; it is not a trivial exercise to interpret the information they contain. For example it is often difficult to identify precisely where genes are located, where they begin and end, what features allow one gene to be highly expressed and another weakly. In order to help us interpret and fully exploit the genome sequences it is invaluable to be able to identify all the RNA molecules that the genome encodes, the transcriptome. This has recently become far more straightforward, with the advent of new sequencing technologies that allow us to obtain hundred of millions of short sequences very rapidly and relatively cheaply. These data can then be analysed by sophisticated computational techniques to build a detailed picture of the genomes function. From this we can establish all the different genes that are present, how they behave under different conditions and how they are organised. The aim of this project is to utilise these sequencing approaches to look at the transcriptome of a fungus, Aspergillus nidulans. Although this organism does occasionally cause disease, particularly in individuals suffering from a rare genetic disorder called Chronic Granulomatous disease, it is primarily employed as a model for understanding fundamental biological systems and in particular closely related species of major importance. These include: Aspergillus fumigatus which is an important allergen, often being associated with sick building syndrome, and the major cause of invasive aspergillosis, a life threatening infection in severely immune-compromised patients with a high mortality rate (25-90%). Unfortunately, the effectiveness of the currently available treatments is limited and diagnosis is problematic. Controlling Aspergillus flavus is important to prevent food spoilage, because of its ability to produce aflatoxin, the most potent carcinogen know. Aspergillus niger is the source of most citric acid used in soft drinks and is also used for both the production of proteins and as a source of enzymes for the food industry. Aspergillus oryzae is also used to manufacture of many traditional fermented Japanese food products, such as soy sauce and saki as well as in biotechnology. The aim of this project is therefore to develop a much greater appreciation of how the Aspergillus genome is organised and functions, allowing us to better understand the fundamental nature of these organisms. The potential is that by improving our understanding of Aspergillus biology we will be better equipped to detect, control and eradicate them where necessary and exploit their potential in developing new biotechnological processes and products.