Detection of pathogenicity related regulatory motif in Ascomycete fungi.

Abstract:

In recent years with the advent of many genome sequences, studying cis-regulatory elements based on comparative genomics has increasingly gained popularity. This approach known as phylogenetic footprinting (PF) is based on the assumption that among phylogenetically related species, the regulating sequences in the upstream regions of orthologous genes are selectively conserved by evolution. Within the Ascomycete class (to which belongs Saccharomyces cerevisiae) the intergenic sequences of many orthologous gene families have found to be enriched in the same regulatory elements (1). The Ascomycete comprises a heterogeneous group of species, containing both pathogenic and non pathogenic species. In this study we wanted to use PF in order to search for motifs differentially present in the pathogenic orthologs but absent in the non pathogenic ones. Starting from the annotated genome of Saccharomyces cerevisiae, we identified for each gene in the yeast genome its orthologs and their corresponding upstream regions in 5 other fungal species of varying phylogenetic distance (human pathogen Aspergilus nidulans and plant pathogens: Magnaporthe grisea, Mycosphaerella fijiensis and Ustilago maydis; non-pathogenic specie: Neurospora crassa). Orthologous mapping was based on the genome wide alignment method TBA (3). Intergenic sequences which appeared conserved among the pathogenic species but which were absent from the non pathogenic ones were subjected to Gibbs sampling (Blocksampler (2)) in order to further refine the alignments (4). Regulatory elements differentially present in pathogenic fungi point …

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