Research

Research at CCDM Bioinformatics encompasses genome analysis of agriculturally-important fungal pathogens and host crop species, and bioinformatic investigation of the underlying biology of their interaction during infection. Our research has described the first analysis of the genomes of several species of agricultural and economic importance. They have defined a broad genetic basis for the biological activities of these organisms and formed a major foundational resource that has facilitated numerous subsequent studies by empowering agricultural molecular biologists to adopt high-throughput reverse genetics approaches in the study of these species. Our research has then taken these resources and via comparative genomics contributed novel insights in the field of fungal genomics. Specifically, the first observation of ‘mesosynteny’ and development of novel algorithms for its characterisation and wider analysis. Also, the development of widely-adopted software for the analysis of a mutagenesis process called repeat-induced point mutation (RIP). These are major drivers of evolution in fungal pathogens and form the pillars of our current efforts in investigating pathogenicity adaptation and developing informed bioinformatics methods to accurately predict fungal genes that cause plant disease.

Recently, CCDM Bioinformatics student Alison Testa has developed and published highly accurate gene-prediction software for fungi: CodingQuarry.

We are also developing other novel techniques for the prediction of fungal pathogenicity genes, based on predicted 3D structures of proteins and by the inspection of RIP-influenced regions of fungal genomes.

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Dr James Hane, Senior Research Fellow, Program Leader, CCDM Bioinformatics program, Centre for Crop & Disease Management