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Analysing telomeric structural variation of Aspergillus fumigatus isolates using long- and short- read sequencing

Aspergillus fumigatus is an opportunistic fungal pathogen that causes infection in the immunocompromised and those with chronic respiratory disease. Aspergillus fumigatus causes a wide spectrum of infection ranging from colonisation through to deep tissue infection called invasive aspergillosis (IA). We have a large collection of A. fumigatus isolates from patients post lung transplantation and with chronic respiratory diseases and have analysed a proportion using short-read whole genome sequencing methodology. We have some data that indicate that genetic variation (single nucleotide polymorphisms) in the A. fumigatus isolates is related to whether the isolates are colonizers or cause invasive disease. However, the WGS sequencing using short-read technology has limitations, in that it cannot resolve some of the highly variable genome areas. These highly variable genome areas are primarily located at the end of chromosomal areas and are called telomeres. In fungi species, telomeres are increasingly being shown to contain important virulence gene clusters and transposable elements that influence gene expression levels. In recent years, the advent of long-read sequencing technology has made it possible to examine the telomeres and determine their genetic sequence. In this project the student will use a combination of long- and short- read sequencing data and bioinformatics tools, to analyse some of the A. fumigatus isolates for telomeric variations and analyse their association with IA. The importance of this work is to determine specific genes associated with IA with a view to developing new drug targets. In this research the student will learn sequencing techniques, bio-informatics skills, and report and manuscript writing. The student will have access to departmental infrastructure and advice from other researchers..
Essential criteria: 
Minimum entry requirements can be found here:
Aspergillus, aspergillosis, whole genome sequencing, virulence, molecular, genetic, immunocompromised, fungus, fungal
Available options 
Masters by research
Time commitment 
Top-up scholarship funding available 
Physical location 
Burnet Institute with Monash University in Melbourne, Australia.

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