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Bioinformatic genome analysis of the necrotrophic wheat-pathogenic fungus Phaeosphaeria nodorum and related Dothideomycete fungi

Hane, James (2011) Bioinformatic genome analysis of the necrotrophic wheat-pathogenic fungus Phaeosphaeria nodorum and related Dothideomycete fungi. PhD thesis, Murdoch University.

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      Abstract

      Phaeosphaeria nodorum (anamorph: Stagonospora nodorum) is the causal agent of Stagonospora nodorum blotch (SNB, syn. glume blotch) in wheat. P. nodorum is estimated to cause up to 31% wheat yield loss worldwide. Within Australia it is the primary pathogen of wheat and is estimated to cause losses of $108 million per annum. The genome assembly of P. nodorum was sequenced in 2005 and was the first species in the class Dothideomycetes, a significant fungal taxon containing several major phytopathogens, to be publically released. The P. nodorum genome database has since evolved from basic sequence data into a powerful resource for studying the SNB host-pathogen interaction and advancing the understanding of fungal genome structure. The genes of P. nodorum have been annotated to a high level of accuracy and now serve as a model dataset for comparative purposes. P. nodorum gene annotations have been refined by a combination of several techniques including manual curation, orthology with related species, expressed sequence tag (EST) alignment, and proteogenomics. Analysis of the repetitive DNA in the P. nodorum genome lead to the development of software for the analysis of repeat-induced point mutation (RIP), a fungal-specific genome defence mechanism, which was a major improvement upon previous methods. Comparative genomics between P. nodorum and related species has highlighted a novel pattern of genome sequence conservation between filamentous fungi called ‘mesosynteny’ and has lead to the development of novel 'genome finishing' strategies.

      Publication Type: Thesis (PhD)
      Murdoch Affiliation: School of Veterinary and Biomedical Sciences
      Supervisor: Oliver, Richard, Howlett, Barbara and Rouxel, Thierry
      URI: http://researchrepository.murdoch.edu.au/id/eprint/5803
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