Alternaria blotches of pome fruits are economically important and the species concepts of these EC listed non-European isolates are not well defined. Morphologically similar toxin producing Alternaria pathogens have also emerged on other hosts and Alternaria species have been intercepted on plant material in the UK recently. Moreover, the range of toxins produced by various isolate groups, their role in pathogenicity and host interactions are yet to be fully established. Lack of resolution of the commonly used molecular markers necessitates the use of innovative approaches to address these issues and develop robust phylogenetic systematics and diagnostic methodologies. Recent advances in the application of DNA-based methodologies are revolutionising fungal phylogenetic systematics. Genome sequences are now available from nearly 60 fungi including two Alternaria species. Based on this data, 246 ortholog clusters of single copy genes have recently been identified as potential species markers, providing an ideal opportunity to test and develop new methodologies (Marthey et al., 2008, BMC Bioinformatics). It is possible that similar speciation processes occur in unrelated plant-pathogenic fungi of agricultural importance, as they are subject to the same recent, extreme agro-ecological selection pressures thus enhancing the generic value of this approach. Warwick HRI have used a combination of genotypic and phenotypic characters to identify and define fungal pathogens (Sreenivasaprasad and Talhinhas, 2005; Talhinhas et al., 2008). We have also developed molecular
methodologies to identify and analyse the expression of functionally important genes in fungi including microarray based gene profiling (Muthumeenakshi et al., 2007; Sreenivasaprasad et al., unpublished). The proposed PhD studentship project based at Warwick HRI will be co-supervised by Fera staff who have expertise in Alternaria pathogens posing plant health risk (PH0171). This will also enable wider links with international, EU (e.g. QBOL) and UK fungal DNA barcoding projects/ approaches.
The overall aims are:
1) to develop molecular methodologies to resolve population-species boundaries in EC regulated Alternaria pathogens, understand risks and develop diagnostic assays for pathogen
monitoring based on multidisciplinary approaches such as phylogenetics, gene expression, phenotyping and their integration using statistical models;
2) to understand speciation processes leading to improved phylogenetic systematic structure in Alternaria pathogens;
3) to explore potential links with wider fungal barcoding type initiatives.
Specific objectives are:
1) To identify phylogenetically informative loci exploiting comparative genomics of fungal sequence databases.
2) To analyse the presence and expression of pathogenicity-related genes in relation to host range/specificity and differentiate pathogenic and non-pathogenic forms
3) To characterise EC listed Alternaria pathogens originating from pome fruits and related pathogens from other important crops using molecular methodologies and phenotypic assays
4) To integrate genotype-phenotype data to define population-species boundaries and develop diagnostic methodologies, contributing to improved systematics