Fungal Genomics and Biosecurity

Non-Technical Summary: Non-Technical Summary: Fungi are the predominant pathogens of plants. A continued safe and secure food and fiber supply in the US requires effective management of plant diseases caused by fungal pathogens. Rapid response to a new disease threat from either endemic or introduced fungal strains requires reliable methods for pathogen identification. Research outlined in this proposal is directed toward identifying DNA regions associated with pathogenicity and fitness and determining the forces that impact the evolution of these traits. Completion of research outlined in this proposal is necessary to locate specific DNA regions that can be used to identify individuals within a population and to distinguish between endemic and introduced fungal plant pathogens. <P> Approach: The common theme in this proposal is locating specific DNA regions associated with virulence or toxin production that can be used for reliable identification of pathogenic individuals within a population. We plan to use a computational computational package called GenomeHistory to analyze gene duplication and gene family expansion as a way to elucidate the determinants of pathogenicity and provide a means to track genome changes. In Aspergillus, bottom-up approaches will be used to examine the evolutionary processes that have given rise to the specific organization and function of genes in the aflatoxin gene pathway. To do this, we will identify nucleotide sequence variation within coding and noncoding portions of the aflatoxin gene cluster in population samples of A. flavus or A. parasiticus. The phylogenetic history of populations will be reconstructed using all available sequence information. To enhance the power of phylogenetic analyses, variation from population samples will be categorized as base substitutions, insertion or deletion motifs, phylogenetically informative or uninformative, transitions versus transversions for base substitutions and replacement versus synonymous amino acid changes for substitutions in coding region. Comparative genomics and gene expression profiling will be used to obtain a better understanding of the evolution of secondary metabolism, its regulatory elements and its linkage to fungal development. A direct comparison of A. flavus and A. nidulans should reveal conserved and diverged regulatory controls in secondary metabolic pathways, particularly AF and ST pathways. We are also interested in the genomic comparison between A. flavus and A. oryzae. We have shown that these two fungi are almost identical in genome structure. However, A. flavus does contain about 300 genes that are not present in A. oryzae. Within this set of unique genes may be genes for pathogenicity. Gene expression analysis and functional genomics will be used to characterize the function of these unique genes. The design and development of taxon-specific probes for identification of plant pathogenic fungi that reside in soil and will provide new tools for examining their ecology and epidemiology across time and space. We propose to develop an expanded DNA-sequence database framework for rapid detection of dominant fungal groups from different soils and phylogenetic-based probes will be designed and tested for their ability to detect these fungi. Our initial efforts will focus on the design probes for detection of the most commonly encountered lineages of soil fungi from agricultural soils. We propose to develop methods that will complement previously funded research to target genes in the quinic acid cluster. Quantitative PCR methods using multiple probes will be used to assay taxonomic structure as a prelude to development and testing of microarray-based systems for detection and identification of fungi from soil.