Functional Genomics, Genetics and Bioinformatics of Cereal Rust Fungi

Summary

  1. De Novo genome assembly using third generation sequencing
  2. RNA-seq based genomic annotation for cereal rust fungi
  3. Comparative genomics of cereal robust isolates in pursuit of avirulence genes
  4. Dissecting the evolutionary relationship of cereal rust fungi using next generation sequencing
  5. Exploring fungicide insensitivity through functional genomics

Supervisor(s)

Dr Jingqin Wu

Research Location

School of Life and Environmental Sciences

Program Type

Masters/PHD

Synopsis

Based on long-read sequencing, high quallity reference genomes will be built up for cereal rust fungi.  These genomes will then be annotated using both de novo and genome-guided transcriptome assemblies generated from RNA-seq.  These reference genomes lay a foundation for comparative collection of rust isolates using next generation sequencing.  These short reads will be mapped to the reference genomes and genetic variants will be detected.  Comparison of the genetic variants between isolates with different virulence profile will help to identify the avirulence genes.  Phylogenetic analysis of the whole genome variants across the collection of the isolates will elucidate the evolution history of these strains.  Fungicide insensitivity, somatic hybridisation, and other biological themes can be explored using these data sets.

Additional Information

The student will be based in Camden for the duration of this project.

HDR Inherent Requirements

In addition to the academic requirements set out in the Science Postgraduate Handbook, you may be required to satisfy a number of inherent requirements to complete this degree. Example of inherent requirement may include:

- Confidential disclosure and registration of a disability that may hinder your performance in your degree;
- Confidential disclosure of a pre-existing or current medical condition that may hinder your performance in your degree (e.g. heart disease, pace-maker, significant immune suppression, diabetes, vertigo, etc.);
- Ability to perform independently and/or with minimal supervision;
- Ability to undertake certain physical tasks (e.g. heavy lifting);
- Ability to undertake observatory, sensory and communication tasks;
- Ability to spend time at remote sites (e.g. One Tree Island, Narrabri and Camden);
- Ability to work in confined spaces or at heights;
- Ability to operate heavy machinery (e.g. farming equipment);
- Hold or acquire an Australian driver’s licence;
- Hold a current scuba diving license;
- Hold a current Working with Children Check;
- Meet initial and ongoing immunisation requirements (e.g. Q-Fever, Vaccinia virus, Hepatitis, etc.)

You must consult with your nominated supervisor regarding any identified inherent requirements before completing your application.

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Keywords

next generation sequencing, third generation sequencing, Bioinformatics, Comparative genomics, transcriptomes, rust secretome, SNP, genome wide association, crop disease, crop protection, host-pathogen interaction, avirulence gene, effector, fungicide insensitivity, somatic hybridisation, Evolution, phylogenetic analysis, population genetics

Opportunity ID

The opportunity ID for this research opportunity is: 2458