Scabies mite genome project
Project type
PhD
| Supervisor(s) | Division | |
| (Primary) | Bioinformatics | .(JavaScript must be enabled to view this email address) |
| (Co-supervisor) | Bioinformatics | .(JavaScript must be enabled to view this email address) |
Details of project
The scabies mite, Sarcoptes scabiei, is an arachnid that burrows into human skin causing infections. Along with other parasitic infections, these contribute to the high burden of disease in many remote Indigenous communities. Secondary infection of scabies lesions by bacteria, such as Staphylococcus and Group A Streptococcus, may lead to rheumatic fever with associated heart and kidney problems.
In collaboration with the Menzies School of Population Health in Darwin and the Queensland Institute of Medical Research, we are sequencing the ~100Mb genome of a model pig scabies mite, as well mites from patients from different areas in the Northern Territory. The closely related house dust mite will also be sequenced. This project will focus on improving the de novo assembly of the genome, developing annotations, and investigating the evolution of the scabies mite.
In particular, we will investigate the changes between the parasitic scabies mite, which burrows into skin and modulates host immunity and the house dust mite, which lives on dead skin cells. Additionally, we will be involved in efforts by our collaborators to investigate the genetic basis of scabies-resistance to acaricides.
Project references
- Walton et al. Scabies: new future for a neglected disease. Adv Parasitol. 2004 57:309-76
- Holt et al. Parasitic diseases of remote Indigenous communities in Australia. Int J Parasitol. 2010 40(10):1119-26
- Gnerre S et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA 2011 108:1513–1518.
Research interests
Our research interests are in the area of biological sequence analysis. This is an area of bioinformatics where ideas from mathematics, statistics and computer science are applies to the analysis of genome, transcript or protein sequence data. We frequently work in close partnership with the biologists and clinicians who generate the data.
Much of our efforts are now focused on the analysis of next generation sequence data and the development of new or boutique methods to improve analyses. A secondary focus of our group is computational comparative genomics. Here we use of sequence data from multiple species to learn about the evolution of genes related to disease. This has also been the basis of approaches to sensitive genome searching that we have developed and applied to study genes in malaria and to discover novel genes in mammalian genomes.
Selected publications
- Warren et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 453(7192):175-83.
- Mikkelsen et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007 447(7141):167-77
Research theme
Infectious diseases
Scientific discipline
- Bioinformatics
- Genomics
Keywords
Next generation sequencing; indigenous health; evolution; de novo assembly