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Insights into the genome and secretome of Didymella pinodes, the causal agent of Ascochyta blight of pea

Kessie, Francis (2013) Insights into the genome and secretome of Didymella pinodes, the causal agent of Ascochyta blight of pea. PhD thesis, Murdoch University.

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Ascochyta blight disease is one of the most important diseases of field pea worldwide and causes considerable damage and yield losses. Four fungal species namely, Didymella pinodes (anamorph, Peyronellaea pinodes syn: Mycosphaerella pinodes), Phoma pinodella (syn: Peyronellaea pinodella), Ascochyta pisi and Phoma koolunga are responsible for the disease and can cause the disease individually or co-occur in a field or lesion. All the pathogens belong to the family Didymellaceae within the fungal order Pleosporales. The family also includes causal agents of Ascochyta blight in other pulses such as chickpea, lentil, and faba bean. Didymella pinodes is the most prominent and damaging of the Ascochya blight pathogens of pea and therefore the focus of this study. Designing effective strategies for disease control in the D. pinodes pea pathosystem has been very difficult. Only relatively low levels of resistance to the pathogen are found within the primary gene pool of pea. There is a limited understanding of the genetic and biochemical bases of pathogenicity and lack of genetic and genomics tools/sequence. The goal of this study was to elucidate molecular factors that are employed by D. pinodes for pathogenicity.

Isolates of D. pinodes were recovered from infected pea leaves in Medina, the Western Australia site for breeding pea cultivars resistant to Ascochyta blight disease in 2007. The isolates’ phylogeny was confirmed based on sequence analysis of the ITS, LSU and TEF1 genes. One of the isolates, M07-4 causing typical Ascochyta blight symptoms was chosen as a reference.

A combination of biochemical methods were used to provide the first evidence that the fungus secretes proteinaceous compounds in culture that can induce necrosis on pea. Subsequently, the proteins were partially purified and are between the size ranges of 10 -50 kDa. To facilitate the identification of the secreted proteins and to reveal other pathogenicity genes that might be present in the fungus, a genome draft of the fungus was acquired. The genome draft comprised of 2,258 scaffolds spanning 32.87 Mbp and contains 11,752 genes models of 50 amino acids or more. The draft sequence was generated entirely using the Illumina Solexa platform. A total of 1,365 genes were validated through proteogenomics curation of gene models and comparative genomic analysis. In silico analysis of the genome coupled with proteomics analysis of the culture filtrates produced by the fungus have identified a number of interesting pathogenicity candidates.

This study is the most comprehensive molecular and sequence analysis conducted on aspects of pathogenicity of any of the pathogens within the pea “Ascochyta complex” and on a causal agent of Ascochyta blight of legumes. It therefore serves as a key reference for further studies on D. pinodes, the other causal pathogens of the pea Ascochyta blight and the Didymellaceae pathogens in general.

Item Type: Thesis (PhD)
Murdoch Affiliation(s): School of Veterinary and Life Sciences
Notes: Note to the author: If you would like to make your thesis openly available on Murdoch University Library's Research Repository, please contact: Thank you.
Supervisor(s): Oliver, Richard and Lichtenzveig, Judith
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