PROJECT

Computational genomics: Understanding the genome

Using computational approaches to analyse plant genome data

There is a huge demand for experienced genome bioinformatics scientists. We offer training in assembling and analysing diverse plant genomes using next generation DNA sequence data and advanced computational methods.

With the rapid growth in DNA sequencing technology, there is a bottleneck in applying this data to gain a greater understanding of plant biology. In addition, as more and more genomes have been sequenced, there has been a general decline in the genome assembly quality. We work in several areas of genome bioinformatics, with a focus on crops and their adaptation to predicted climate change scenarios, but also work on plant pests and pathogens, as well as species of environmental or evolutionary significance.

Current research areas include:

  • The assembly and validation of several crop genomes of agricultural importance, working with international consortia. These crops include wheat, canola and the vegetable Brassicas, chickpea, clover, asparagus, pea, and lentil. We also assemble and validate genomes of aphid pests, fungal pathogens and environmentally or evolutionary interesting species such as coral and seagrass.
  • Genome annotation, the prediction of gene structures in the genome and the estimation of their potential function is the first step towards understanding what all the A, C, G and T strings mean. We are working on several genome annotation projects.
  • Genome variation characterisation includes the discovery and characterisation of single nucleotide polymorphisms, gene presence/absence characterisation (and pan-genome construction) through to large-scale genome rearrangements. Once these variations have been characterised, they can be associated with heritable traits and the information used to accelerate crop improvement. These variations also provide a historical account of species evolution and selection.
  • Epigenetics provides an additional regulatory layer in the genome, and this is becoming increasingly acknowledged as a potential area for crop yield improvement and providing resilience to climate relates stress.
  • Databases and visualisation tools are essential for the interrogation of the vast amount of genomics data currently being generated.

Projects could involve research in any of the above areas and would depend on the interests and skills of the student, as well as the status of ongoing projects within the group.

For more background information, see the suggested readings below. 

Research team leader: Professor David Edwards

 

I am a Professor in Plant Biology, UWA with an interest in understanding the structure, function and evolution of plant genomes and the application of this knowledge to accelerate crop improvement. While my background is in wet lab genomics, my team are now all computational, applying data produced from the latest genomics technologies to better understand plants. We work on diverse crop species such as wheat, canola and chickpea as well as wild crop relatives and non-crop plants such as seagrass.

PhD opportunities

Interested in becoming part of this project? Complete the following steps to submit your expression of interest:

Step 1 - Check criteria

General UWA PhD entrance requirements can be found on the Future Students website

Requirements specific to this project:

The projects are all computer based, using dedicated high performance computing systems and software. Potential students should have an excellent understanding of Linux and command line operations. Additional training in the use of high performance computing will be provided.

Step 2 - Submit enquiry to research team leader

Step 3 - Lodge application

After you have discussed your project with the research team leader, you should be in a position to proceed to the next step of the UWA application process: Lodge an applicationDifferent application procedures apply to domestic and international students.

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CRICOS Code: 00126G
Updated
Tuesday, 23 October 2018 1:33 AM (this date excludes nested assets)
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